65. K. G. Sprenger, A. Prakash, G. Drobny, and J. Pfaendtner “Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations  Langmuir, Article ASAP, 2017, DOI: 10.1021/acs.langmuir.7b02868

64. A. Prakash, J. Pfaendtner, J. Chun, C. J. Mundy “Quantifying the Molecular-Scale Aqueous Response to the Mica Surface”  J. Phys. Chem. C, 2017, 121 (34) 18496-18504. DOI: 10.1021/acs.jpcc.7b03229

63. A. Prakash, K. G. Sprenger, J. Pfaendtner. “Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation” Biochemical and Biophysical Research Communications, in press, 2017.

62. K. G. Sprenger, J. G. Plaks, J. L. Kaar, J. Pfaendtner. “Elucidating sequence and solvent design targets to protect and stabilize enzymes for biocatalysis in ionic liquids”  Phys. Chem. Chem. Phys., 2017, 19, 17426-17433. DOI: 10.1039/C7CP03013D

61. J. Smith, K. G. Sprenger, R. Liao, A. Joseph, E. Nance, J. Pfaendtner. Determining dominant driving forces affecting controlled protein release from polymeric nanoparticles” Biointerphases 12, 02D412, 2017; doi: 10.1116/1.4983154

60. X. Ma, S. Zhang, F. Jiao, C. J. Newcomb, Y. Zhang, A. Prakash, Z. Liao, M. D. Baer, C. J. Mundy, J. Pfaendtner, A. Noy, C-L. Chen, J. J. Yoreo. Tuning crystallization pathways through sequence engineering of biomimetic polymers, Nature Materials 2017. Advance on line publication. DOI: 10.1038/NMAT4891

59. K. Palunas, K.G. Sprenger, T. Weidner, J. Pfaendtner. Effect of an ionic liquid/air Interface on the structure and dynamics of amphiphilic peptidesJ. Mol. Liquids, 2017, 236, 404. DOI: 10.1016/j.molliq.2017.04.027

58. C. D. Fu, L. F. L. Oliveira, J. Pfaendtner,Assessing Generic Collective Variables for Determining Reaction Rates in Metadynamics Simulations J. Chem. Theory Comput.2017, 13 (3), 968. DOI: 10.1021/acs.jctc.7b00038

57. C. D. Fu, L. F. L. Oliveira, J. Pfaendtner, “Determining Energy Barriers and Selectivities of a Multi-Pathway System With Infrequent Metadynamics”, J. Chem. Phys., 2017, 146, 014108. DOI: 10.1063/1.4971800

56. H. Lutz, V. Jaeger, M. Bonn, J. Pfaendtner, T. Weidner, “Acetylation dictates the morphology of nanophase biosilica precipitated by a 14-amino acid leucine-lysine peptide”, J. Peptide Sci., 2017, 23:147, DOI10.1002/psc.2960

55. V. Jaeger, J. Pfaendtner, “Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations”, J. Phys. Chem. B, 2016, 120(47), 12079-12087. DOI: 10.1021/acs.jpcb.6b09410

54. W. A. Beckner, Y. He, J. Pfaendtner, “Chain Flexibility in Self-Assembled Monolayers Affects Protein Adsorption and Surface Hydration, a Molecular Dynamics Study”, J. Phys. Chem. B., 2016, 120(40), 10423-10432. DOI: 10.1021/acs.jpcb.6b05882

53. H. Tung, J. Pfaendtner, “Kinetics and mechanism of ionic-liquid induced protein unfolding: Application to the model protein HP35”, Mol. Syst. Des. Eng., 2016, 1, 382-390. DOI: 10.1039/C6ME00047A

52. B. Hough, D. T. Schwartz, J. Pfaendtner, Detailed kinetic modeling of lignin pyrolysis for process optimizationIECR, 2016, 55(34), 9147-9153. DOI: 10.1021/acs.iecr.6b02092

51. R. Pandey, K. Usui, R.A. Livingstone, S.A. Fischer, J. Pfaendtner, E. H. G. Backus, Y. Nagata, J. Fröhlich-Nowoisky, L. Schmüser, S. Mauri, J.F. Scheel, D.A. Knopf, U. Pöschl, M. Bonn, T. Weidner, Ice Nucleating Bacteria Control Order and Dynamics of Interfacial Water”, Science Advances, 2016, 2(4), e1501630. DOI: 10.1126/sciadv.1501630

50. K.G. Sprenger, Y. He, J. Pfaendtner, “Probing how defects in self-assembled monolayers affect peptide adsorption with molecular simulation”, in Molecular Modeling and Simulation, 2016, 21-35, eds Randy Q. Snurr, Claire Adjiman and David Kofke. DOI: 10.1007/978-981-10-1128-3_2

49. K.G. Sprenger, J. Pfaendtner, “Using molecular simulation to study biocatalysis in ionic liquids, (invited contribution), in to Methods in Enzymology, 2016, 577, 419-441, ed. Gregory A. Voth. DOI: 10.1016/bs.mie.2016.05.020

 48. K.G. Sprenger and J. Pfaendtner, Strong Electrostatic Interactions Lead to Entropic Stabilization of Peptides on Surfaces”, Langmuir, 2016, 32 (22), 5690–5701. DOI: 10.1021/acs.langmuir.6b01296

47. C. Krumm, J. Pfaendtner, P.J. Dauenhauer, “Millisecond Pulsed Films Unify the Mechanisms of Cellulose Fragmentation”, Chemistry of Materials, 2016, 28(9), 3108-3114. DOI:10.1021/acs.chemmater.6b00580

46. D. Beck, J.M. Carothers, V. Subramanian, J. Pfaendtner, “Data science: Accelerating innovation and discovery in chemical engineering”, AIChE Journal, 2016, 62(5), 1402-1416. DOI: 10.1002/aic.15192

45. M. Donovan, Y. Yimmer, J. Pfaendtner, E. Backus, M. Bonn, T. Weidner, “Ultrafast reorientational dynamics of leucine at the air-water interface”, JACS, 2016, 138 (16), 5226–5229. DOI: 10.1021/jacs.6b01878

44. K. G. Sprenger, A. Choudhury, J. Kaar, J. Pfaendtner , “Lytic Polysaccharide Monooxygenases ScLPMO10B and ScLPMO10C Are Stable in Ionic Liquids as Determined by Molecular Simulations”, J. Phys. Chem. B., 2016, 120(16), 3863-3872. DOI: 10.1021/acs.jpcb.6b01688

43. K. Fleming, P. Tiwary, J. Pfaendtner, “New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations”, J. Phys. Chem. A., 2015, 120(2), 299-305. DOI: 10.1021/acs.jpca.5b10667 [ACS Editors Choice]

42. T. Bereau, W.F. Drew Bennett, J. Pfaendtner, M. Deserno, M. Karttunen, “Folding and insertion thermodynamics of the transmembrane WALP peptide”, J. Chem. Phys., 2015, 143, 243127. DOI: 10.1063/1.4935487

41. J. Pfaendtner, M. Bonomi, “Efficient sampling of high-dimensional free-energy landscapes with Parallel Bias Metadynamics”, J. Chem. Theor. Comput., 2015, 11(11), 5062-5067. DOI: 10.1021/acs.jctc.5b00846

40. H. Lutz, V. W. Jaeger, R. Berger, M. Bonn, J. Pfaendtner, T. Weidner, “Biomimetic Growth of Ultrathin Silica Sheets Using Artificial Amphiphilic Peptides”, Advanced Materials Interfaces, 2015, 2(17), e1500282. DOI: 10.1002/admi.201500282

39. P. de la Iglesia, V. W. Jaeger, Y. Xi, J. Pfaendtner, L. D. Pozzo, “Structure Characterization and Properties of Metal-Surfactant Complexes Dispersed in Organic Solvents”, Langmuir, 2015, 31(33), 9006-9016. DOI: 10.1021/acs.langmuir.5b02071

38. Z. Levine, S.A. Fischer, J. E. Shea and J. Pfaendtner, “Trp-Cage Folding on Organic Surfaces”, J. Phys. Chem. B., 2015, 119(3), 10417-10425. DOI: 10.1021/acs.jpcb.5b04213

37. R. Elder, J. Pfaendtner, A. Jayaraman, “Effect of hydrophobic and hydrophilic surfaces on the stability of double-stranded DNA”, Biomacromolecules, 2015, 16(6), 1862-1869.  DOI: 10.1021/acs.biomac.5b00469

36. K. G. Sprenger, V. W. Jaeger, J. Pfaendtner, “The General AMBER Force Field (GAFF) Can Accurately Predict Thermodynamic and Transport Properties of Many Ionic Liquids” J. Phys. Chem. B., 2015, 119(18), 5882-5895. DOI: 10.1021/acs.jpcb.5b00689

35. P. Burney, E. M. Norwald, K. Hickman, J. L. Kaar, J. Pfaendtner, “Molecular dynamics investigation of the ionic liquid/enzyme interface: Application to engineering enzyme surface charge” Proteins, 2015, 83(4), 670-680. DOI: 10.1002/prot.24757

34. G. Newbloom, S. Hoffmann, A. West, M. Gile, P. Sista, H. Cheung, C. Luscombe, J. Pfaendtner, L. D. Pozzo, “Solvatochromism and Conformational Changes in Fully Dissolved Poly(3-alkylthiophene)s”, Langmuir, 2015, 31(1), 458-468. DOI: 10.1021/la503666x

33. V. Jaeger, P. Burney, J. Pfaendtner, “Comparison of Three Ionic Liquid Tolerant Cellulases by Molecular Dynamics”, Biophysical Journal, 2015, 108(4), 880-892. DOI: 10.1016/j.bpj.2014.12.043

32. K. Fleming, J. Matthei, J. Pfaendtner, “A new graduate level seminar to prepare students for the next step in their career”, Chemical Engineering Education, 2015, 49(1) 29-37.

31. S. Zheng, J. Pfaendtner, “Enhanced sampling of chemical and biochemical reactions with metadynamics”, Molecular Simulation, 2015, 41(1-3), 55-72. DOI: 10.1080/08927022.2014.923574 [invited review]

30. J. E. Baio, A. Zane, V. Jaeger, A.M. Roehrich, H. Lutz, J. Pfaendtner, G P. Drobny, T Weidner, “Diatom mimics: directing the formation of biosilica nano-particles by controlled folding of lysine-leucine peptides”, JACS, 2014, 136(43), 15134-15137. DOI: 10.1021/ja5078238

29. S. Zheng, J. Pfaendtner “Car–Parrinello Molecular Dynamics + Metadynamics Study of High-Temperature Methanol Oxidation Reactions Using Generic Collective Variables”, J. Phys. Chem. C., 2014, 118(20), 10764-10770. DOI: 10.1021/jp500398k

28. Z. Jarin and J. Pfaendtner, “Ionic Liquids Can Selectively Change the Conformational Free-Energy Landscape of Sugar Rings” J. Chem. Theor. Comput., 2014, 10(2), 507-510. DOI: 10.1021/ct4010036

27. P. Burney, N. White, J. Pfaendtner, “Structural Effects of Methionine Oxidation on Isolated Subdomains of Human Fibrin D and αC regions” PLoS One, 2014, 9(1), e68981.

26. A. Paulson, B. Hough, C. L. Williams, A. R. Teixeira, D. T. Schwartz, J. Pfaendtner, P. J. Dauenhauer, “Fast Pyrolysis of Wood Particles: Spatiotemporally-Resolved Diffuse Reflectance in situ Spectroscopy of Particles (STR-DRiSP)” Chem Sus Chem, 2014, 7(3), 765-776

25. A. Barducci, J. Pfaendtner,  M. Bonomi, “Tackling Sampling Challenges in Biomolecular Simulations”  In Molecular Modeling of Proteins, Kukol, A., Ed. Springer New York: New York, NY, 2015, pp 151-171.

24. K. L. Fleming, J. Pfaendtner, “Characterizing the catalyzed hydrolysis of β-1,4 glycosidic bonds using DFT”, J. Phys. Chem. A, 2013, 117(51), 14200-14208.

23. M. Deighan, J. Pfaendtner, “Exhaustively Sampling Peptide Adsorption with Metadynamics”, Langmuir, 2013, 29(25), 7999-8009. DOI: 10.1021/la4010664

22. A. White, A. Keefe, J. R. Ella-Menye, A. Nowinski, Q. Shao, J. Pfaendtner, S. Jiang, “Insights into Solvated Salt Bridges”, J. Phys. Chem. B, 2013, 117(24), 7254-7259.  

21. V. Jaeger, J. Pfaendtner, “Structure, Dynamics and Activity of Xylanase Solvated in Binary Mixtures of Ionic Liquid and Water”, ACS Chemical Biology, 2013, 117(9), 2662-2670. DOI: 10.1021/cb3006837

20. P. Burney, J. Pfaendtner “Structural and dynamic features of Candida rugosa Lipase1 in Water, Octane, Toluene, and Ionic Liquids BMIM-PF6 and BMIM-NO3”, J. Phys. Chem. B, 2013, 117, 2662-2670.

19. M. Deighan, M. Bonomi, J. Pfaendtner, “Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble”, J. Chem. Theor. Comp., 2012, 8, 2189-2192. DOI: 10.1021/ct300297t

18. J. Pfaendtner, N. Volkmann, D. Hanein, P. Dalhaimer, T.D. Pollard, G. A. Voth, “Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation”, J. Mol. Biol, 2012, 416 (1), 148-161.

17. J. Pfaendtner, E. M. De La Cruz, G. A. Voth, “Actin Filament Remodeling by actin depolymerization factor/cofilin,” Proc. Natl. Acad. Sci. USA, 2010, 97 (16), 7299-7304.

16. J. Pfaendtner, E. Lyman, T. D. Pollard, G. A. Voth, “Structure and dynamics of the actin filament,” J. Mol. Biol., 2010, 396 (2), 252-263. [selected for cover article]    

15. J. Pfaendtner, D. Branduardi, M. Parrinello, T. D. Pollard,  G. A. Voth, Nucleotide-Dependent Conformational States of Actin,” Proc. Natl. Acad. Sci. USA, 2009, 106 (31), 12723-12728.

14. Z. Zhang, J. Pfaendtner, A. Grafmüller, G. A. Voth, Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models, Biophys. J., 2009, 97 (8), 2327-2333.

13. J. Pfaendtner, Chemical and Biochemical Kinetics and Macrokinetics , in Chemical Engineering and Chemical Process Technology, [Eds. Ryzhard Pohorecki, John Bridgwater, Rafiqul GANI], in Encyclopedia of Life Support Systems (EOLSS), 2009, Developed under the Auspices of the UNESCO, EOLSS Publishers, Oxford, UK.

12. J. Pfaendtner, G. A. Voth,“Molecular Dynamics Simulation and Coarse-grained Analysis of the UnactivatedArp2/3Complex,”Biophys. J., 200895 (11), 5324-5333.

 11. E. Lyman, J. Pfaendtner, G. A. Voth, “Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins,” Biophys. J., 2008, 95 (9), 4183-4192.

10. Z. Zhang, L. Lu, W. G. Noid, V. Krishna, J. Pfaendtner, G. A. Voth, “A Systematic Methodology for Defining Coarse-grained Sites in Large Biomolecules,” Biophys. J., 2008, 95 (11), 5073-5083.

9. X. Yu, J. Pfaendtner, L. J. Broadbelt, “Ab Initio Study of Acrylate Polymerization Reactions: Methyl Methacrylate and Methyl Acrylate Propagation,” J. Phys. Chem. A, 2008, 112 (29), 6772-6782.

8. J. Pfaendtner, L. J. Broadbelt, “Mechanistic Modeling of Lubricant Degradation Part 1: Structure-Reactivity Relationships for Free-Radical Oxidation,” Ind. Eng. Chem. Res., 2008, 47 (9), 2886-2896.

7. J. Pfaendtner, L. J. Broadbelt, Mechanistic Modeling of Lubricant Degradation Part 2: The Autoxidation of Decane and Octane,” Ind. Eng. Chem. Res., 200847(9), 2897-2904.

6. M. Siniawski, N. Saniei, J. Pfaendtner, “Tribological Degradation of Two Vegetable-Based Lubricants at Elevated Temperatures,” J. Synth. Lubr., 2007, 24 (3), 167-169.

5. J. Pfaendtner, L. J. Broadbelt, “Contra-thermodynamic Behavior in Intermolecular Hydrogen Transfer of Alkylperoxy Radicals, ROO· + R’H,” ChemPhysChem, 2007, 8 (13), 1969-1978.

4. J. Pfaendtner, X. Yu, and L. J. Broadbelt, “The 1D Hindered Rotor Approximation,” Theor. Chem. Acc., 2007, 118 (5-6), 881-898.

3.  J. Pfaendtner, L. J. Broadbelt, “Elucidation of Structure-Reactivity Relationships in Hindered Phenols Via Quantum Chemistry and Transition State Theory,” Chem. Eng. Sci., 2007, 62 (18-20), 5232-5239.

2. J. Pfaendtner, X. Yu, L. J. Broadbelt, “Quantum Chemical Investigation of Low- Temperature Intramolecular Hydrogen Transfer Reactions of Hydrocarbons,” J. Phys. Chem. A, 2006, 110 (37), 10863-10871.

1. L. J. Broadbelt, J. Pfaendtner, “Lexicography of Kinetic Modeling of Complex Reaction Networks AIChE. J., 2005, 51 (8), 2112-2121.