The Faculty


Selected honors and awards

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)


Ragon Postdoctoral Fellow, MIT, 2010-12 (Arup Chakraborty)
PhD, Princeton, 2005-10 (Thanos Panagiotopoulos, Pablo Debenedetti, Yannis Kevrekidis)
MEng, Imperial College London, 2001-05

Research interests

We work on problems in molecular and materials science using theory and tools from statistical thermodynamics, molecular simulation, applied mathematics, bioinformatics, high performance computing, and machine learning (usually manifold or deep learning).

Our research interests lie broadly in the investigation of equilibrium and dynamic properties of soft matter, with specific interests in the self-assembly of biological and bio-inspired materials, machine learning enhanced sampling, inference and control of biomolecular folding and assembly landscapes, collective variable estimation, statistically optimal sampling and free energy estimation, vaccine design, and protein engineering.

Selected publications

S. Chen, C.W. Peterson, J.A. Parker, S.A. Rice, A.L. Ferguson*, and N.F. Scherer “Data-driven reaction coordinate discovery in overdamped and non-conservative systems: Application to optical matter structural isomerization” Nat. Commun. 12 2548 (2021) [ ]

A.L. Ferguson* and R. Ranganathan “100th Anniversary of Macromolecular Science Viewpoint: Data-driven protein design” ACS Macro. Lett. 10 327-340 (2021) [ ]

W. Alvarado, J. Moller, A.L. Ferguson*, and J.J. de Pablo “Tetranucleosome interactions drive chromatin folding” ACS Cent. Sci. 7 6 1019–1027 (2021) [ ]

 Y. Ma, J. Aulicino, and A.L. Ferguson* “Inverse design of self-assembling diamond photonic lattices from anisotropic colloidal clusters” J. Phys. Chem B 125 9 2398-2410 (2021) [ ]

Y. Yang; H. Ying, Z. Li, J. Wang, Y. Chen. B. Luo, D.L. Gray, A.L. Ferguson, Q. Chen, Y. Z, and J. Cheng “Near quantitative synthesis of urea macrocycles enabled by bulky N-substituent” Nat. Commun. 12 1572 (2021) [ ]

Y. Xia, Z. Song, T. Xue, S. Wei, L. Zhu, Z. Tan, Y. Yang, H. Fu, Y. Jiang, Y. Lin, Y. Lu, A.L. Ferguson*, and J. Cheng “Accelerated polymerization of N-carboxyanhydrides catalyzed by crown ether” Nat. Commun. 12 732 (2021) [ ]

C.H. Fry, B. Peters, and A.L. Ferguson “Pushing and pulling: A dual pH triggered heme peptide assembly” J. Phys. Chem. B 125 5 1317-1330 (2021) [ ]

 E.Y. Lee, L.C. Chan, H. Wang, J. Lieng, M. Hung, Y. Srinivasan, J. Wang, J. Waschek, A.L. Ferguson, K.-F. Lee, N.Y. Yount, M.R. Yeaman, and G.C.L. Wong “Mood-modulating neuropeptide PACAP is potently induced during infection” Proc. Natl. Acad. Sci. USA 118 1 e1917623117 (2020) [ ]

 M. Zasloff “An ancient neuropeptide defends the brain against infection” PNAS 118 5 e2023990118 (2020)

A.L. Ferguson* “Editorial: The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry” J. Phys. Chem B 124 9767−9772 (2020) [ ]

B. Sharma, Y. Ma, A.L. Ferguson*, and A.P. Liu “In search of a novel chassis material for synthetic cells: Emergence of synthetic peptide compartment” Soft Matter 16 10769 (2020) [ ]

M. Topel and A.L. Ferguson* “Reconstruction of protein structures from single molecule time series” J. Chem. Phys. 153 194102 (2020) [ ]