Pfaendtner Research Group - Publications

2019
2018
2017
2016
2015
2014
2013
2012

2019

Fantastic Liquids and Where to Find Them: Optimizations of Discrete Chemical Space W. Beckner and J. Pfaendtner, J. Chem. Inf. Model.
Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces M. Mao, J. Sampath, K.G. Sprenger, G. Drobny, J. Pfaendtner, Langmuir
Diagnosing the Impact of External Electric Fields Chemical Kinetics: Application to Toluene Oxidation and Pyrolysis C.D. Fu, Y. He, J. Pfaendtner, J. Phys. Chem. A.
A Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces E.L. Buckle, A. Prakash, M. Bonomi, J. Sampath, J. Pfaendtner, G.P. Drobny, JACS

2018

Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water D. Verreault, S. Alamdari, S. Roeters, R. Pandey, J. Pfaendtner, T. Weidner, Phys. Chem. Chem. Phys.
Inhibition of the Exoglucanase CEL7A by a Douglas-fir Condensed Tanin KR Oleson, KG Sprenger, J. Pfaendtner, DT Schwartz JCPB
Biasing Smarter, Not Harder, By Partitioning Collective Variables Into Families in Parallel Bias Metadynamics A Prakash, C. Fu, M Bonomi, J Pfaendtner JCTC
Density functional tight-binding and infrequent metadynamics can capture entropic effects in intramolecular hydrogen transfer reactions LFL Oliveira, C Fu, J Pfaendtner JCP
Lifting the Curse of Dimensionality on Enhanced Sampling of Reaction Networks with Parallel Bias Metadynamics C Fu, J Pfaendtner JCTC
Peptoid backbone flexibility dictates its interaction with water and surfaces: A molecular dynamics investigation A. Prakash, M. Baer, C.J. Mundy, J. Pfaendtner, in press Biomacromolecules
Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations K. G. Sprenger, A. Prakash, G. Drobny, J. Pfaendtner, Langmuir
Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation A. Prakash, K. G. Sprenger, J. Pfaendtner, Biochem. Biophys. Res. Commun.

2017

LK peptide side chain dynamics at interfaces are independent of secondary structure M. A. Donovan, H. Lutz, Y. Y. Yimer, J. Pfaendtner, M. Bonn, T. Weidner, Phys. Chem. Chem. Phys.
Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids S. R. Summers, K. G. Sprenger, J. Pfaendtner, J. Marchant, M. F. Summers, J. L. Kaar, J. Phys. Chem. B.
Redefining the Protein–Protein Interface: Coarse Graining and Combinatorics for an Improved Understanding of Amino Acid Contributions to the Protein–Protein Binding Affinity J. K. Smith, S. Jiang, J. Pfaendtner, Langmuir
Quantifying the Molecular-Scale Aqueous Response to the Mica Surface A. Prakash, J. Pfaendtner, J. Chun, C. J. Mundy, J. Phys. Chem. C.
Thiolated Lysine-Leucine Peptides Self-Assemble into Biosilica Nucleation Pits on Gold Surfaces H. Lu, Y. Yimer, R. Berger, M. Bonn, J. Pfaendtner, T. Weidner, Advanced Materials Interfaces
Data Science for Chemical Engineers D. Beck, J. Pfaendtner, J. Carothers, V. Subramanian, Chem. Eng. Progress
Enhancing the Oxidation of Toluene with External Electric Fields: A Reactive Molecular Dynamics Study S. Tan, T. Xia, Y. Shi, J. Pfaendtner, Z. Shuangliang, Y. He, Scientific Reports
Determining dominant driving forces affecting controlled protein release from polymeric nanoparticles K.G. Sprenger, J. Smith, R. Liao, A. Joseph, E.A. Nance, J. Pfaendtner, Biointerphases
Elucidating sequence and solvent specific design targets to protect and stabilize enzymes for biocatalysis in ionic liquids K.G. Sprenger, J.G. Plaks, J. Kaar, J. Pfaendtner, PhysChemChemPhys
Effect of an Ionic Liquid/Air Interface on the Structure and Dynamics of Amphiphilic Peptides K.G. Sprenger, K. Palunas, T. Weidner, J. Pfaendtner, J. Mol. Liq.
The Structure of the Diatom Silaffin Peptide R5 within Freestanding Two-Dimensional Biosilica Sheets H. Lutz, V. Jaeger, L. Schmüser, M. Bonn, J. Pfaendtner, T. Weidner, Ang. Chem. Int. Ed.
Assessing Generic Collective Variables for Determining Reaction Rates in Metadynamics Simulations C.D. Fu, L.F.L., Oliveira, J. Pfaendtner, J. Chem. Theor. Comput.
Tuning crystallization pathways through sequence- engineering of biomimetic polymers X. Ma, S. Zhang, F. Jiao, C. Newcomb, Y. Zhang, A. Prakash, Z. Liao, M. Baer, C. Mundy, J. Pfaendtner, A. Noy, C. Chen, J. De Yoreo, Nature Materials
Determining Energy Barriers and Selectivities of a Multi- Pathway System With Infrequent Metadynamics C.D. Fu, L.F.L. Oliveira, J. Pfaendtner, J Chem Phys.
Acetylation dictates the morphology of nanophase biosilica precipitated by a 14-amino acid leucine-lysine peptide H. Lutz, V. Jaeger, M. Bonn, J. Pfaendtner, T. Weidner, J. Peptide Sci.

2016

Application of machine learning to pyrolysis reaction networks: reducing model solution time to enable process optimization B. Hough, D.A.C. Beck, D.T. Schwartz, J. Pfaendtner, Comp and Chem Eng.
Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations V. Jaeger, J. Pfaendtner, J. Phys. Chem. B
Chain Flexibility in Self-Assembled Monolayers Affects Protein Adsorption and Surface Hydration, a Molecular Dynamics Study W. A. Beckner, Y. He, J. Pfaendtner, J. Phys. Chem. B.
Kinetics and mechanism of ionic-liquid induced protein unfolding: Application to the model protein HP35 H. Tung, J. Pfaendtner, Mol. Syst. Des. Eng.
Ice Nucleating Bacteria Control Order and Dynamics of Interfacial Water 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, Science Advances
Probing how defects in self-assembled monolayers affect peptide adsorption with molecular simulation K.G. Sprenger, Y. He, J. Pfaendtner, in Molecular Modeling and Simulation
Strong Electrostatic Interactions Lead to Entropic Stabilization of Peptides on Surfaces K.G. Sprenger and J. Pfaendtner, Langmuir
Millisecond Pulsed Films Unify the Mechanisms of Cellulose Fragmentation C. Krumm, J. Pfaendtner, P.J. Dauenhauer, Chemistry of Materials
Data science: Accelerating innovation and discovery in chemical engineering D. Beck, J.M. Carothers, V. Subramanian, J. Pfaendtner, AIChE Journal
Ultrafast reorientational dynamics of leucine at the air-water interface M. Donovan, Y. Yimmer, J. Pfaendtner, E. Backus, M. Bonn, T. Weidner, JACS
Lytic Polysaccharide Monooxygenases ScLPMO10B and ScLPMO10C Are Stable in Ionic Liquids as Determined by Molecular Simulations K.G. Sprenger, A. Choudhury, J. Kaar, J. Pfaendtner, J. Phys. Chem. B.

2015

New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations K. Fleming, P. Tiwary, J. Pfaendtner, J. Phys. Chem. A.
Folding and insertion thermodynamics of the transmembrane WALP peptide T. Bereau, W.F. Drew Bennett, J. Pfaendtner, M. Deserno, M. Karttunen, J. Chem. Phys.
Efficient sampling of high-dimensional free-energy landscapes with Parallel Bias Metadynamics J. Pfaendtner, M. Bonomi, J. Chem. Theor. Comput.
Biomimetic Growth of Ultrathin Silica Sheets Using Artificial Amphiphilic Peptides H. Lutz, V.W. Jaeger, R. Berger, M. Bonn, J. Pfaendtner, T. Weidner, Advanced Materials Interfaces
Structure Characterization and Properties of Metal-Surfactant Complexes Dispersed in Organic Solvents P. de la Iglesia, V.W. Jaeger, Y. Xi, J. Pfaendtner, L. D. Pozzo, Langmuir
Trp-Cage Folding on Organic Surfaces Z. Levine, S.A. Fischer, J.E. Shea and J. Pfaendtner, J. Phys. Chem. B.
Effect of hydrophobic and hydrophilic surfaces on the stability of double-stranded DNA R. Elder, J. Pfaendtner, A. Jayaraman, Biomacromolecules
The General AMBER Force Field (GAFF) Can Accurately Predict Thermodynamic and Transport Properties of Many Ionic Liquids K. G. Sprenger, V.W. Jaeger, J. Pfaendtner, J. Phys. Chem. B.
Molecular dynamics investigation of the ionic liquid/enzyme interface: Application to engineering enzyme surface charge P. Burney, E. M. Norwald, K. Hickman, J. L. Kaar, J. Pfaendtner, Proteins
Solvatochromism and Conformational Changes in Fully Dissolved Poly(3-alkylthiophene)s G. Newbloom, S. Hoffmann, A. West, M. Gile, P. Sista,; H. Cheung, C. Luscombe, J. Pfaendtner, L. D. Pozzo, Langmuir
Comparison of Three Ionic Liquid Tolerant Cellulases by Molecular Dynamics V. Jaeger, P. Burney, J. Pfaendtner, Biophysical Journal
A new graduate level seminar to prepare students for the next step in their career K. Fleming, J. Matthei, J. Pfaendtner, Chemical Engineering Education
Enhanced sampling of chemical and biochemical reactions with metadynamics S. Zheng, J. Pfaendtner, Molecular Simulation

2014

Diatom mimics: directing the formation of biosilica nano-particles by controlled folding of lysine- leucine peptides J. E. Baio, A. Zane, V. Jaeger, A.M. Roehrich, H. Lutz, J. Pfaendtner, G P. Drobny, and T Weidner, JACS
Car–Parrinello Molecular Dynamics + Metadynamics Study of High- Temperature Methanol Oxidation Reactions Using Generic Collective Variables S. Zheng, J. Pfaendtner, J. Phys. Chem. C.
Ionic Liquids Can Selectively Change the Conformational Free-Energy Landscape of Sugar Rings Z. Jarin and J. Pfaendtner, J. Chem. Theor. Comput.
Structural Effects of Methionine Oxidation on Isolated Subdomains of Human Fibrin D and αC regions P. Burney, N. White, J. Pfaendtner, PLoS One
Fast Pyrolysis of Wood Particles: Spatiotemporally-Resolved Diffuse Reflectance in situ Spectroscopy of Particles (STR-DRiSP) A. Paulson, B. Hough, C. L. Williams, A. R. Teixeira, D. T. Schwartz, J. Pfaendtner, P. J. Dauenhauer, Chem Sus Chem

2013

Characterizing the catalyzed hydrolysis of β-1,4 glycosidic bonds using DFT K. L. Fleming, J. Pfaendtner, J. Phys. Chem. A
Exhaustively Sampling Peptide Adsorption with Metadynamics M. Deighan, J. Pfaendtner, Langmuir
Insights into Solvated Salt Bridges A. White, A. Keefe, J. R. Ella-Menye, A. Nowinski, Q. Shao, J. Pfaendtner, S. Jiang, J. Phys. Chem. B
Structure, Dynamics and Activity of Xylanase Solvated in Binary Mixtures of Ionic Liquid and Water V. Jaeger and J. Pfaendtner, ACS Chemical Biology
Structural and dynamic features of Candida rugosa Lipase1 in Water, Octane, Toluene, and Ionic Liquids BMIM-PF6 and BMIM-NO3 P. Burney and J. Pfaendtner, J. Phys. Chem. B

2012

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble M. Deighan, M. Bonomi, J. Pfaendtner, J. Chem. Theor. Comp.
Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation J. Pfaendtner, N. Volkmann, D. Hanein, P. Dalhaimer, T.D. Pollard, G.A. Voth, J. Mol. Biol