Stacks Image 550
BOOK CHAPTERS
1. G.R. Hart and A.L. Ferguson "Viral fitness landscapes: A physical sciences perspective" in "Systems Immunology: An introduction to modeling methods for scientists" J. Das, C. Jayaprakash (eds.) Taylor and Francis (in press, 2017) [ISBN-10: 1498717403]
CONFERENCE PAPERS
2. A. Kononov, P. Bellon, T. Bretl, A.L. Ferguson, G.L. Herman, K.A. Kilian, J.A. Krogstad, C. Leal, C.R. Maass, A. Schleife, J.K. Shang, D.R. Trinkle, and M. West "Computational Curriculum for MatSE Undergraduates" Paper presented at 2017 American Society for Engineering Education (ASEE) 124th Annual Conference & Exposition, Columbus, OH, June 25-28 2017 [pdf] [https://peer.asee.org/28060]

1. R.A. Mansbach, G.L. Herman, M. West, D.R. Trinkle, A.L. Ferguson, and A. Schleife "WORK IN PROGRESS: Computational Modules for the MatSE Undergraduate Curriculum" Paper presented at American Society for Engineering Education (ASEE) 123rd Annual Conference & Exposition, New Orleans, LA, June 26-29 2016 [pdf] [http://dx.doi.org/10.18260/p.27214]
JOURNAL ARTICLES
* Designates corresponding author.
2017
40. J. Wang and A.L. Ferguson* "Nonlinear machine learning in simulations of soft and biological materials" Mol. Sim. (submitted, 2017)
Invited review article for the “Free Energy Simulations” special issue

39. J. Wang and A.L. Ferguson "A study of the morphology, dynamics, and folding pathways of ring polymers with supramolecular topological constraints using molecular simulation and nonlinear manifold learning" Macromolecules (submitted, 2017)

38.
M.W. Lee, E.Y. Lee, G.H. Lai, N.W. Kennedy, A.E. Posey, W. Xian, A.L. Ferguson, R.B. Hill, and G.C.L. Wong "Molecular motor Dnm1 synergistically induces membrane curvature to facilitate mitochondrial fission" ACS Cent. Sci. (submitted, 2017)

37.
A.W. Long and A.L. Ferguson* "Landmark diffusion maps (L-dMaps): Accelerated manifold learning out-of-sample extension" Appl. Comput. Harmon. Anal. (in press, 2017) [http://dx.doi.org/10.1016/j.acha.2017.08.004]

36. E.Y. Lee, M.W. Lee, B.M. Fulan, A.L. Ferguson*, and G.C.L. Wong "What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?" Interface Focus (in press, 2017)
RSC Interface Focus invited mini-review

35. E.Y. Lee, G.C.L. Wong, and A.L. Ferguson* "Machine learning discovery and design of membrane-active peptides" Bioorg. Med. Chem. (in press, 2017) [http://dx.doi.org/10.1016/j.bmc.2017.07.012]
Invited mini-review for "Peptide Therapeutics" symposium-in-print

34. Z. Song, R.A. Mansbach, R. Baumgartner, K.-C. Shih, H. He, N. Zheng, X. Ba, Y. Huang, D. Mani, Y. Lin, M.-P. Nieh, A.L. Ferguson*, L. Yin, and J. Cheng "Modulation of polypeptide conformation through donor-acceptor transformation of side-chain hydrogen bonding ligands" Nat. Commun. 92 8 1-8 (2017) [pdf] [SI] [movieS1] [movieS2] [http://dx.doi.org/10.1038/s41467-017-00079-5]

33. W.F. Reinhart, A.W. Long, M.P. Howard, A.L. Ferguson, and A.Z. Panagiotopoulos "Machine learning for autonomous crystal structure identification" Soft Matter 13 4733-4745 (2017) [pdf] [http://dx.doi.org/10.1039/c7sm00957g]

32. R.A. Mansbach and A.L. Ferguson* "Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow" Org. Biomol. Chem. 15 26 5484-5502 (2017) [pdf] [SI] [movieM1] [movieM2] [movieM3] [movieM4] [movieM5] [movieM6] [movieM7] [movieM8] [http://dx.doi.org/10.1039/C7OB00923B]
Invited submission for "Peptide Materials" special issue
Selected as 2017 HOT Article in Organic and Biomolecular Chemistry
Featured as the cover article of Organic and Biomolecular Chemistry 15 26 (2017)
Stacks Image p1662_n2
31. J. Wang, M. Gayatri, and A.L. Ferguson* "Mesoscale simulation and machine learning of asphaltene aggregation phase behavior and molecular assembly landscapes" J. Phys. Chem. B 121 18 4923-4944 (2017) [pdf] [SI] [http://dx.doi.org/10.1021/acs.jpcb.7b02574]

30. A.L. Ferguson* "BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method" J. Comput. Chem. 38 18 1583-1605 (2017) [pdf] [code] [http://dx.doi.org/10.1002/jcc.24800]

29. R.A. Mansbach and A.L. Ferguson* "Coarse-grained molecular simulation of the hierarchical self-assembly of π-conjugated optoelectronic peptides" J. Phys. Chem. B 121 7 1684-1706 (2017) [pdf] [SI] [forcefield] [http://dx.doi.org/10.1021/acs.jpcb.6b10165]
2016
28. E.Y. Lee, B.M. Fulan, G.C.L. Wong, and A.L. Ferguson* "Mapping membrane activity in undiscovered peptide sequence space using machine learning" Proc. Natl. Acad. Sci. USA 113 48 13588-13593 (2016) [pdf] [SI] [http://dx.doi.org/10.1073/pnas.1609893113]

27. C.D. Allen, M.Y. Chen, A.Y. Trick, D. Thanh Le, A.L. Ferguson*, and A.J. Link "Thermal unthreading of the lasso peptides astexin-2 and astexin-3" ACS Chem. Biol. 11 11 3043-3051 (2016) [pdf] [SI] [movieS1] [movieS2] [movieS3] [movieS4] [http://dx.doi.org/10.1021/acschembio.6b00588]

26. J. Wang and A.L. Ferguson* "Mesoscale simulation of asphaltene aggregation" J. Phys. Chem. B 120 32 8016-8035 (2016) [pdf] [SI] [http://dx.doi.org/10.1021/acs.jpcb.6b05925]

25. A.W. Long, C.L. Phillips, E. Jankowski, and A.L. Ferguson* "Nonlinear machine learning and design of reconfigurable digital colloids" Soft Matter 12 7119-7135 (2016) [pdf] [SI] [movieS1] [movieS2] [movieS3] [http://dx.doi.org/10.1039/C6SM01156J]

24. R.A. Mansbach, A.L. Ferguson, K.A. Kilian, J.A. Krogstad, C. Leal, A. Schleife, D.R. Trinkle, M. West, and G.L. Herman "Reforming an undergraduate materials science curriculum with computational modules" J. Mater. Educ. 38 3-4 161-174 (2016) [pdf]

23. J. Hu and A.L. Ferguson* "Global graph matching using diffusion maps" Intelligent Data Analysis 20 3 637-654 (2016) [pdf] [http://dx.doi.org/10.3233/IDA-160824]

22. J. Wang and A.L. Ferguson* "Nonlinear reconstruction of single-molecule free energy surfaces from univariate time series" Phys. Rev. E 93 032412 (2016) [pdf] [http://link.aps.org/doi/10.1103/PhysRevE.93.032412]

21. B.A. Thurston, J.D. Tovar, and A.L. Ferguson* "Thermodynamics, morphology, and kinetics of early-stage self-assembly of pi-conjugated oligopeptides" Mol. Sim. 42 12 955-975 (2016) [pdf] [movie1] [movie2] [http://dx.doi.org/10.1080/08927022.2015.1125997]
2015
20. G.R. Hart and A.L. Ferguson* "Empirical fitness models for hepatitis C virus immunogen design" Physical Biology 12 066006 (2015) [pdf] [SI] [http://dx.doi.org/10.1088/1478-3975/12/6/066006]

19. M. Xiong, M.W. Lee, R. Mansbach, Z. Song, Y. Bao, R.M. Peek Jr., C. Yao, L.-F. Chen, A.L. Ferguson*, G.C.L. Wong, and J. Cheng "Helical antimicrobial polypeptides with radial amphiphilicity" Proc. Natl. Acad. Sci. USA 112 43 13155-13160 (2015) [pdf] [appendix] [SI] [movieS1] [movieS2] [movieS3] [http://dx.doi.org/10.1073/pnas.1507893112]

18. A.W. Long, J. Zhang, S. Granick, and A.L. Ferguson* "Machine learning assembly landscapes from particle tracking data" Soft Matter 11 8141-8153 (2015) [pdf] [SI] [movieS1] [movieS2] [http://dx.doi.org/10.1039/C5SM01981H]

17. 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) [pdf] [SI] [http://dx.doi.org/10.1063/1.4914144]
Ranked as one of the most read Biological Molecules and Networks articles of the year

16. 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) [pdf] [http://dx.doi.org/10.1103/PhysRevE.91.032705]
2014
15. 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) [pdf] [SI] [http://dx.doi.org/10.1073/pnas.1411499111]

14. B.D. Wall, Y. Zhou, S. Mei, H.A.M. Ardona, 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) [pdf] [SI] [http://dx.doi.org/10.1021/la501999g]

13. 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) [pdf] [SI] [code] [http://dx.doi.org/10.1371/journal.pcbi.1003776]

12. 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) [pdf] [SI] [http://dx.doi.org/10.1021/la500222y]

11. 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) [pdf] [SI] [http://dx.doi.org/10.1021/jp500350b]
2013
10. 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) [pdf] [SI] [http://dx.doi.org/10.1103/PhysRevE.88.062705]

9. 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) [pdf] [SI] [http://dx.doi.org/10.1371/journal.pone.0080562]

8. 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) [pdf] [SI] [http://dx.doi.org/10.1016/j.immuni.2012.11.022]
Immunity Preview: N. Goonetilleke and A.J. McMichael "HIV-1 Vaccines: Let’s Get Physical” Immunity 38 410-413 (2013) [pdf] [http://dx.doi.org/10.1016/j.immuni.2013.02.017]
Cell Leading Edge Select: L. Gay and N. Neuman "Antiviral Strategies: Building a Better Defense” Cell 153 727-728 (2013) [pdf] [http://dx.doi.org/10.1016/j.cell.2013.04.039]

8_McMichael_perspective_banner

2012
7. 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) [pdf] [SI] [movie1] [movie2] [http://dx.doi.org/10.1063/1.4755750]
Featured on the cover of JCP 137 14 (2012)
Most read regular JCP article in October 2012
Selected as a 2012 Editor’s Choice Article

6_CoverImage

2011
6. 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) [pdf] [http://dx.doi.org/10.1016/j.cplett.2011.04.066]
Featured on the cover of Chem. Phys. Lett. 509 1 (2011)

6_CPLCover

5. 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) [pdf] [SI] [http://dx.doi.org/10.1063/1.3574394]

2010
4. 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) [pdf] [SI] [movie] [http://dx.doi.org/10.1016/j.bpj.2010.08.073]

3. 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) [pdf] [SI] [movie] [http://dx.doi.org/10.1073/pnas.1003293107]
2009
2. 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) [pdf] [SI] [http://dx.doi.org/10.1021/jp811229q]
2006
1. E. Guibal, T. Vincent, E. Touraud, S. Colombo, and A.L. Ferguson "Oxidation of hydroquinone to p-benzoquinone catalyzed by Cu(II) supported on chitosan flakes" J. Appl. Polym. Sci. 100 4 3034-3043 (2006) [pdf] [http://dx.doi.org/10.1002/app.23702]