Publications

View Jim Pfaendtner’s Google Scholar profile for a complete listing of citations and work.

Recent highlights

• Fantastic Liquids and Where to Find Them: Optimizations of Discrete Chemical Space W. Beckner and J. Pfaendtner, J. Chem. Inf. Model.

  • This paper shows an adaptive learning and design approach using genetic algorithm to discover new ionic liquids outside of known property windows

• Closing the Gap Between Modeling and Experiments in the Self-assembly of Biomolecules at Interfaces and in Solution, Janani Sampath, Sarah Alamdari, and Jim Pfaendtner, Chemistry of Materials

  • This review article highlights integration of simulation and experiment in studies related to interfacial phenomena of biomolecules

• Molecular recognition and specificity of biomolecules to titanium dioxide from molecular dynamics simulations, Janani Sampath, Andrew Kullman, Rachel Gebhart, Gary Drobny & Jim Pfaendtner, npj Computational Materials

  • In this article, we describe a detailed study of peptide binding thermodynamics to TiO2 surfaces, reconciling longstanding experimental disagreements about the relationship between binding energy and surface chemistry

• Sequence–Structure–Binding Relationships Reveal Adhesion Behavior of the Car9 Solid-Binding Peptide: An Integrated Experimental and Simulation Study , Brittney Hellner, Sarah Alamdari, Harley Pyles, Shuai Zhang, Arushi Prakash, Kayla G. Sprenger, James J. De Yoreo, David Baker, Jim Pfaendtner, and François Baneyx, JACS

FEATURED METHODS IN COMPUTATIONAL MOLECULAR SCIENCE

• Exhaustively Sampling Peptide Adsorption With Metadynamics, Michael Deighan, Jim Pfaendtner, Langmuir

• Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics, Jim Pfaendtner and Massimiliano Bonomi, JCTC

• Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble, Michael Deighan, Massimiliano Bonomi, and Jim Pfaendtner, JCTC

• New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations, Kelly L. Fleming, Pratyush Tiwary, and Jim Pfaendtner, J. Phys. Chem. A

• The General AMBER Force Field (GAFF) Can Accurately Predict Thermodynamic and Transport Properties of Many Ionic Liquids, K. G. Sprenger, Vance W. Jaeger, and Jim Pfaendtner, J. Phys. Chem B