Principal Investigator
Andrew L Ferguson
Professor of Molecular Engineering
Vice Dean for Education and Outreach
Co-Founder, Evozyne Inc.
Deputy Editor-in-Chief, Molecular Systems Design & Engineering (MSDE)
Chair, AIChE Computational Molecular Science and Engineering Forum (CoMSEF)
Director, CECAM-US-CENTRAL
Contact:
Pritzker School of Molecular Engineering
University of Chicago
5640 South Ellis Avenue
Chicago, IL 60637
t: (773) 702-5950
Education:
Ragon Postdoctoral Fellow, MIT, 2010-12 (Arup Chakraborty)
PhD, Princeton, 2005-10 (Thanos Panagiotopoulos, Pablo Debenedetti, Yannis Kevrekidis)
MEng, Imperial College London, 2001-05
Selected Honors and Awards:
Professorial ACMM Chair of Computational Science, University of Amsterdam (2022-23)
Dreyfus Foundation Machine Learning in the Chemical Sciences and Engineering Award (2020)
IChemE Junior Moulton Medal (2018/19)
UIUC College of Engineering Dean’s Award for Excellence in Research (2017)
AIChE CoMSEF Young Investigator Award for Modeling & Simulation (2016)
ACS COMP OpenEye Outstanding Junior Faculty Award (2015)
National Center for Supercomputing Applications Faculty Fellow (2015-16)
ACS PRF Doctoral New Investigator Award (2014)
NSF CAREER Award (2014)
IChemE North America Young Chemical Engineer of the Year (2013)
Links:
Postdoctoral Researchers
Dr. Siva Dasetty
Postdoctoral Associate, Pritzker School of Molecular Engineering
Research Interests:
Coarse-grained modeling of polarizable nanoparticle assembly, microtubule dynamics, membrane proteins and enhanced sampling methods development
Email: sivadasetty@uchicago.edu
Dr. Armin Shayesteh Zadeh
Postdoctoral Associate, Pritzker School of Molecular Engineering
Research Interests:
Enhanced sampling calculations and data-driven discovery of small molecule binding agents
Email: arminsh@uchicago.edu
Dr. Soumajit Dutta
Postdoctoral Associate, Pritzker School of Molecular Engineering
Research Interests:
Data-driven enhanced sampling of crystal defect formation and motion
Email: dutta1@uchicago.edu
Dr. Siddarth Achar
Postdoctoral Associate, Pritzker School of Molecular Engineering
Research Interests:
High-throughput virtual screening and data-driven design of sensitive and selective molecular sensors
Email: sachar@uchicago.edu
Graduate Researchers
Max Topel
Graduate Research Assistant, Pritzker School of Molecular Engineering
Research Interests:
Reconstruction of molecular configurations from experimental time series measurements
Email: maxtopel@uchicago.edu
Mike Jones
Graduate Research Assistant, Pritzker School of Molecular Engineering
Research Interests:
Deep learning and acceleration of slow collective modes in biomolecular folding and assembly
Email: mikejones@uchicago.edu
Yifeng (Oliver) Tang (co-advised w/ Aaron Esser-Kahn)
Graduate Research Assistant, Pritzker School of Molecular Engineering
Research Interests:
Deep and active learning discovery of influenza vaccine adjuvants
Email: yifengt@uchicago.edu
Nicholas Herringer
Graduate Research Assistant, Chemistry
Research Interests:
Molecular modeling of self-assembly pi-conjugated oligopeptides and DNA functionalized nanoparticles
Email: nherringer@uchicago.edu
Kate Johnson (co-advised w/ Nicolas Chevrier)
Graduate Research Assistant, Pritzker School of Molecular Engineering
Research Interests:
Data-driven analysis of intra- and inter-cell immunological signaling pathways.
Email: katej@uchicago.edu
Nikša Praljak (co-advised w/ Rama Ranganathan)
Graduate Research Assistant, Biophysical Sciences
Research Interests:
Deep learning generative models for guided protein engineering
Email: niksapraljak1@uchicago.edu
Jianming Mao
Graduate Research Assistant, Chemistry
Research Interests:
Molecular modeling and design of MOFs and synthetic cell membranes
Email: mjianming@uchicago.edu
Alex Berlaga
Graduate Research Assistant, Chemistry
Research Interests:
Computational design of secondary and tertiary structured peptoids
Email: berlaga@uchicago.edu
Hugh Yeh (co-advised w/ Jun Huang)
MD-PhD Student, Medical Scientist Training Program
Research Interests:
Deep learning generative models for antibody design
Email: hughy@uchicago.edu
Marcia Luna Ramirez Hincapie
Graduate Research Assistant, Pritzker School of Molecular Engineering
Research Interests:
Molecular modeling and engineering of adaptive networks for extreme mechanics
Email: lunaramirez@uchicago.edu
Aniruddha Seal (co-advised w/ Laura Gagliardi)
Graduate Research Assistant, Chemistry
Research Interests:
Multi-scale modeling and enhanced sampling of reaction kinetics in enzymes and heterogeneous catalysts
Email: aniruddhaseal@uchicago.edu
Olabisi Aishat Bello (co-advised w/ Aaron Esser-Kahn)
Graduate Research Assistant, Chemistry
Research Interests:
Data-driven discovery of vaccine adjuvants and immunomodulators
Email: olabisibello@uchicago.edu
Sun Yong Kwon
Graduate Research Assistant, Pritzker School of Molecular Engineering
Research Interests:
Data-driven surrogate models of biomolecular dynamics
Email: sunyongkwon@uchicago.edu
Max Gruschka
Graduate Research Assistant, Pritzker School of Molecular Engineering
Research Interests:
Computational engineering of responsive DNA functionalized nanoparticles
Email: gruschka@uchicago.edu
Srivarshini Ganesan
Graduate Research Assistant, Pritzker School of Molecular Engineering
Research Interests:
Deep generative models for data-driven protein design
Email: srivarshinig@uchicago.edu
Yuhan Wu
Graduate Research Assistant, Pritzker School of Molecular Engineering
Research Interests:
Data-driven design of of new dermotological models and therapies
Email: yuhanwu@uchicago.edu
Undergraduate Researchers
Junhee Lee
BS Candidate, Pritzker School of Molecular Engineering
Email: jlee768@uchicago.edu
Jay Shen
BS Candidate, Physics and Computer Science
Email: jshe@uchicago.edu
Srusti Donapati
BS Candidate, Biological Science and Data Science
Email: srustidonapati@uchicago.edu
Tommy Walsh
BS Candidate, Biology and Computer Science
Email: tmwalsh@uchicago.edu
Group Alumni
Postdoctoral Alumni
Dr. Hythem Sidky
Researcher,
National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD
Email: hsidky@uchicago.edu
Dr. Brandon Peters
Postdoctoral Appointee, Argonne National Laboratory
Email: petersb@uchicago.edu
Dr. Mingfei Zhao
Postdoctoral Appointee, Los Alamos National Laboratory
Email: petersb@uchicago.edu
PhD Alumni
Dr. Andrew W Long
Senior Data Scientist, 3M, Maplewood MN
Email: awlong@mmm.com
Dr. Greg R Hart
Research Scientist, Institute for Disease Modeling, Seattle, WA
Email: gregory.hart@yale.edu
Prof. Jiang Wang
Assistant Professor of Physics, Guizhou Institute
of Technology
Email: jwang110@illinois.edu
Prof. Ré Mansbach
Assistant Professor of Physics, Concordia University
Email: mansbac2@illinois.edu
Dr. Bryce A Thurston III
Postdoctoral Associate, Sandia National Lab
Email: thursto2@illinois.edu
Dr. Wei Chen
Data Scientist, Teza Technologies LLC
Email: weichen9@uchicago.edu
Dr. Yutao Ma
Risk Engineer, Goldman Sachs Inc.
Email: yma3@uchicago.edu
Dr. Walter Alvarado (co-advised w/ Juan de Pablo)
Junior Scientist, NASA
Email: walt@uchicago.edu
Kirill Shmilovich
Machine Learning Engineer, Genentech
Email: kirills@uchicago.edu
Xinran Lian (co-advised w/ Rama Ranganathan)
Email: xlian@uchicago.edu
Shiqi Chen (co-advised w/ Norbert Scherer)
Postdoctoral Researcher, Jason Green Lab, UMass Boston
Email: chen_1777787@outlook.com
Undergraduate Alumni
Jingtian Hu
(2012-13)
PhD Candidate, Materials Science and Engineering, Northwestern University
Yuecheng (Peter) Zhou
(2012-14)
PhD Candidate, Materials Science and Engineering / Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign
Shao Mei
(2013-14)
Epic Medical Records, Verona, WI
Alex Trick
(2013-16)
PhD Candidate, Biomedical Engineering, Johns Hopkins University
Samuel Kaufman
(2014-15)
BS Candidate, Materials Science and Engineering, University of Illinois at Urbana-Champaign
Bridgette LaFaye
(2014-15)
PhD Candidate, Materials Science and Engineering, UC Berkeley
Deepak Mani
(2015-17)
Research Scientist, Broad Institute, Cambridge, MA
Mohit Gayatri
(2016-18)
Application Engineer, Gamma Technologies
Chester Chen
(2016-18)
BS Candidate, Electrical and Computer Engineering, UIUC
Aik-Rui Tan
(2017-18)
PhD Candidate, Materials Science and Engineering, MIT
Olivia Dunne
(2018-20)
BS Candidate, Pritzker School of Molecular Engineering, UChicago
Gillian Shen
(2018-20)
PhD Candidate, UW Seattle
Joseph Aulicino
(2019-21)
BS Candidate, Pritzker School of Molecular Engineering, UChicago
Melody Leung
(2020-22)
BS Candidate, Pritzker School of Molecular Engineering, UChicago
Rohan Kapoor
(2021-22)
BS Candidate, Pritzker School of Molecular Engineering, UChicago
Diya Ghandi
(2022-24)
Algorithmic Development, UBS
Smayan Khanna
(2022-24)
BS Candidate, Pritzker School of Molecular Engineering