Team > Andrew Ferguson
Andrew Ferguson
University of Illinois at Urbana-Champaign
Phone: (217) 300-2354
Web pages:

  • Ragon Postdoctoral Fellow, Department of Chemical Engineering, MIT, 2012
  • Ph.D. Department of Chemical and Biological Engineering, Princeton University 2010
  • M.Eng. Department of Chemical Engineering, Carnegie Mellon University 2004
  • M.Eng., ACGI, Department of Chemical Engineering, Imperial College London 2005

Academic Positions:
  • Assistant Professor of Materials Science and Engineering, UIUC, 2012-present
Research Interests:

Molecular Simulation | Machine Learning | Self-Assembly | Viral Dynamics | Protein Folding
  • Molecular modeling and simulation of biophysical systems at atomistic and coarse-grained resolution
  • Systematic order parameter discovery using linear and nonlinear dimensionality reduction tools
  • Many-body nonlinear learning for the design of self-assembling soft materials
  • Low-dimensional descriptions of viral fitness landscapes and evolutionary dynamics
  • Nonlinear inference of protein folding landscapes from univariate time series data
  • Molecular simulation of the self-assembly of bioorganic electronic polymers and asphaltenes

Selected Publications:
  • A.L. Ferguson, P.G. Debenedetti and A.Z. Panagiotopoulos “Solubility and molecular conformations of n-alkane chains in water” J. Phys. Chem. B 113 18 6405-6414 (2009)
  • A.L. Ferguson, A.Z. Panagiotopoulos, P.G. Debenedetti and I.G. Kevrekidis “Systematic determination of order parameters for chain dynamics using diffusion maps” Proc. Natl. Acad. Sci. USA 107 31 13597-13602 (2010)
  • A.L. Ferguson, S. Zhang, I. Dikiy, A.Z. Panagiotopoulos, P.G. Debenedetti and A.J. Link “An experimental and computational investigation of lasso formation in microcin J25” Biophys. J. 99 9 3056-3065 (2010)
  • A.L. Ferguson, A.Z. Panagiotopoulos, P.G. Debenedetti and I.G. Kevrekidis “Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide” J. Chem. Phys. 134 135103 (2011)
  • A.L. Ferguson, A.Z. Panagiotopoulos, I.G. Kevrekidis and P.G. Debenedetti “Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach” Chem. Phys. Lett. Frontiers 509 1 1-11 (2011)
  • → Featured as the cover article of Chemical Physics Letters 509 1 (2011)
  • A.L. Ferguson, N. Giovambattista, P.J. Rossky, A.Z. Panagiotopoulos and P.G. Debenedetti “A computational investigation of the phase behavior and capillary sublimation of water confined between nanoscale hydrophobic plates” J. Chem. Phys. 137 144501 (2012)
  • → Featured as the cover article of Journal of Chemical Physics 137 (2012)
    → Most read regular Journal of Chemical Physics article in October 2012
    → Selected as a 2012 Journal of Chemical Physics Editor’s Choice article
  • A.L. Ferguson, J.K. Mann, S. Omarjee, T. Ndung’u, B.D. Walker and A.K. Chakraborty “Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design” Immunity 38 606-617 (2013)
  • → Highlighted in an accompanying commentary article: N. Goonetilleke and A.J. McMichael "HIV-1 vaccines: Let’s get physical” Immunity 38 410-413 (2013)
    → Editorial selection as feature in Cell “Select” series on antiviral strategies in Cell 153 4 (2013)
  • A.L. Ferguson, E. Falkowska, L.M. Walker, M.S. Seaman, D.R. Burton and A.K. Chakraborty “Computational prediction of broadly neutralizing HIV-1 antibody epitopes from neutralization activity data” PLOS ONE 8 12 e80562 (2013)
  • K. Shekhar, C.F. Ruberman, A.L. Ferguson, J.P. Barton, M. Kardar, A.K. Chakraborty "Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes" Phys. Rev. E 88 062705 (2013)
  • A.W. Long and A.L. Ferguson “Nonlinear machine learning of patchy colloid self-assembly mechanisms and pathways” J. Phys. Chem. B 118 15 4228-4244 (2014)
  • B.D. Wall, A.E. Zacca, A.M. Sanders, W.L. Wilson, A.L. Ferguson and J.D. Tovar "Supramolecular polymorphism: Tunable electronic interactions within pi-conjugated peptide nanostructures dictated by primary amino acid sequence" Langmuir 30 20 5946-5956 (2014)
  • J.K. Mann, J.P. Barton, A.L. Ferguson, S. Omarjee, B.D. Walker, A.K. Chakraborty and T. Ndung’u "The fitness landscape of HIV-1 gag: Advanced modeling approaches and validation of model predictions by in vitro testing" PLOS Comput. Biol. 10 8 e1003776 (2014)
  • B.D. Wall, Y. Zhou, S. Mei, H.A.M. Ardoña, A.L. Ferguson and J.D. Tovar “Variation of formal hydrogen bonding networks within electronically delocalized pi-conjugated oligopeptide nanostructures” Langmuir 30 (38) 11375–11385 (2014)
  • L. Tang, X. Yang, I. Chaudhury, C. Yao, Q. Yin, Q. Zhou, M. Kwon, L.W. Dobrucki, L.B. Borst, S. Lezmi, W.G. Helferich, A.L. Ferguson, T.M. Fan and J. Cheng "Investigating the optimal size of anticancer nanomedicine" Proc. Natl. Acad. Sci. USA 111 (43) 15344-15349 (2014)
  • G.R. Hart and A.L. Ferguson "Error catastrophe and phase transition in the empirical fitness landscape of HIV" Phys. Rev. E 91 032705 (2015)
  • R.A. Mansbach and A.L. Ferguson "Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics" J. Chem. Phys. 142 105101 (2015)
  • → Ranked as one of the most read Biological Molecules and Networks articles of the year
  • A.W. Long, J. Zhang, S. Granick, and A.L. Ferguson "Machine learning assembly landscapes from particle tracking data" Soft Matter (accepted, 2015)
  • M. Xiong, M.W. Lee, Z. Song, C. Yao, R. Mansbach, A.L. Ferguson, G.C.L. Wong, and J. Cheng "Helical antimicrobial polypeptides with radial amphiphilicity" (in press, 2015)
  • G.R. Hart and A.L. Ferguson "Empirical fitness models for hepatitis C virus immunogen design" (submitted, 2015)
  • J. Wang and A.L. Ferguson "Nonlinear inference of single-molecule free energy surfaces from univariate time series" (submitted, 2015)
  • B.A. Thurston, J.D. Tovar, and A.L. Ferguson “Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides” (submitted, 2015)
  • J. Hu and A.L. Ferguson “Global graph matching by nonlinear manifold learning” Intelligent Data Analysis 20 3 (2016) [to appear Spring 2016]