Jim Pfaendtner (J Pfaendtner)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 73

Top Topics

Machine Learning

Atomic Force Microscopy

Top Venues

The journal of physical chemistry. B

The journal of physical chemistry. A

Langmuir : the ACS journal of surfaces and colloids

Biomacromolecules

This page only lists publications with an associated author ORCID identifier.

Publications

Xin Qi, Jim Pfaendtner
High-Throughput Computational Screening of Solid-Binding Peptides. Journal of chemical theory and computation (2024)
Chenyang Shi, Marlo Zorman, Xiao Zhao, Miquel B Salmeron, Jim Pfaendtner, Xiang Yang Liu, Shuai Zhang, James J De Yoreo
Two-dimensional silk. Science advances 10 (38) (2024)
Ava Waggett, Jim Pfaendtner
Hydrophobic Residues Promote Interfacial Activation of Candida rugosa Lipase: A Study of Rotational Dynamics. Langmuir : the ACS journal of surfaces and colloids (2024)
Marlo Zorman, Christian Phillips, Chenyang Shi, Shuai Zhang, James J De Yoreo, Jim Pfaendtner
Thermodynamic Analysis of Silk Fibroin-Graphite Hybrid Materials and Their Morphology. The journal of physical chemistry. B (2024)
Coco M Mao, Janani Sampath, Jim Pfaendtner
Molecular Driving Forces in the Self-Association of Silaffin Peptide R5 from MD Simulations. Chembiochem : a European journal of chemical biology (2024)
Rishabh Sanghavi, Nadia N Intan, Shaoqu Xie, Hongfei Lin, Jim Pfaendtner
Reaction Pathway Analysis of PET Deconstruction via Methanolysis and Tertiary Amine Catalysts. The journal of physical chemistry. A 128 (29) (2024)
Coco M Mao, Janani Sampath, Jim Pfaendtner
Molecular Driving Forces in the Self-Association of Silaffin Peptide R5 from MD Simulations. Chembiochem : a European journal of chemical biology 25 (11) (2024)
Marlo Zorman, Christian Phillips, Chenyang Shi, Shuai Zhang, James J De Yoreo, Jim Pfaendtner
Thermodynamic Analysis of Silk Fibroin-Graphite Hybrid Materials and Their Morphology. The journal of physical chemistry. B 128 (10) (2024)
Xin Qi, Jim Pfaendtner
High-Throughput Computational Screening of Solid-Binding Peptides. Journal of chemical theory and computation 20 (7) (2024)
Rishabh Sanghavi, Nadia N Intan, Shaoqu Xie, Hongfei Lin, Jim Pfaendtner
Reaction Pathway Analysis of PET Deconstruction via Methanolysis and Tertiary Amine Catalysts. The journal of physical chemistry. A (2024)
Xin Qi, Jim Pfaendtner
High-Throughput Computational Screening of Solid-Binding Peptides. Journal of chemical theory and computation 20 (7) (2024)
Kaylyn Torkelson, Jim Pfaendtner
Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations. Biomacromolecules (2024)
Marlo Zorman, Christian Phillips, Chenyang Shi, Shuai Zhang, James J De Yoreo, Jim Pfaendtner
Thermodynamic Analysis of Silk Fibroin-Graphite Hybrid Materials and Their Morphology. The journal of physical chemistry. B 128 (10) (2024)
Rishabh Sanghavi, Nadia N Intan, Shaoqu Xie, Hongfei Lin, Jim Pfaendtner
Reaction Pathway Analysis of PET Deconstruction via Methanolysis and Tertiary Amine Catalysts. The journal of physical chemistry. A 128 (29) (2024)
Kacper J Lachowski, Huat Thart Chiang, Kaylyn Torkelson, Wenhao Zhou, Shuai Zhang, Jim Pfaendtner, Lilo D Pozzo
Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention. Langmuir : the ACS journal of surfaces and colloids (2023)
Sarah Alamdari, Jim Pfaendtner
Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N -1-Phenylethyl Sidechains. The journal of physical chemistry. B (2023)
Mingfei Zhao, Shuai Zhang, Renyu Zheng, Sarah Alamdari, Christopher J Mundy, Jim Pfaendtner, Lilo D Pozzo, Chun-Long Chen, James J De Yoreo, Andrew L Ferguson
Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes. Biomacromolecules (2023)
Andrew L Ferguson, Jim Pfaendtner
Virtual Special Issue on Machine Learning in Physical Chemistry, Volume 2 ─ Call for Papers. The journal of physical chemistry. A (2023)
Andrew L Ferguson, Jim Pfaendtner
Characteristics of Impactful Machine Learning Contributions to The Journal of Physical Chemistry . The journal of physical chemistry. B 127 (2) (2023)
Andrew L Ferguson, Jim Pfaendtner
Virtual Special Issue on Machine Learning in Physical Chemistry, Volume 2 ─ Call for Papers. The journal of physical chemistry. B (2023)
Andrew L Ferguson, Jim Pfaendtner
Characteristics of Impactful Machine Learning Contributions to The Journal of Physical Chemistry . The journal of physical chemistry. A 127 (2) (2023)
Sarah Alamdari, Kaylyn Torkelson, Xiaoqian Wang, Chun-Long Chen, Andrew L Ferguson, Jim Pfaendtner
Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains. The journal of physical chemistry. B (2023)
Andrew L Ferguson, Jim Pfaendtner
Characteristics of Impactful Machine Learning Contributions to The Journal of Physical Chemistry . The journal of physical chemistry. B 127 (2) (2023)
Orion Dollar, Nisarg Joshi, Jim Pfaendtner, David A C Beck
Efficient 3D Molecular Design with an E(3) Invariant Transformer VAE. The journal of physical chemistry. A (2023)
Sarah Alamdari, Jim Pfaendtner
Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N -1-Phenylethyl Sidechains. The journal of physical chemistry. B (2023)
Nadia N Intan, Jim Pfaendtner
Role of Surface Features on the Initial Dissolution of CH 3 NH 3 PbI 3 Perovskite in Liquid Water: An Ab Initio Molecular Dynamics Study. ACS nano (2023)
Andrew L Ferguson, Jim Pfaendtner
Virtual Special Issue on Machine Learning in Physical Chemistry, Volume 2 ─ Call for Papers. The journal of physical chemistry. A 127 (11) (2023)
Andrew L Ferguson, Jim Pfaendtner
Virtual Special Issue on Machine Learning in Physical Chemistry, Volume 2 ─ Call for Papers. The journal of physical chemistry. B 127 (11) (2023)
Kris Strunge, Tucker Burgin, Thaddeus W Golbek, Steven J Roeters, Jim Pfaendtner, Tobias Weidner
Umbrella-like Helical Structure of α-Synuclein at the Air-Water Interface Observed with Experimental and Theoretical Sum Frequency Generation Spectroscopy. The journal of physical chemistry letters (2023)
Robert G Alberstein, Jesse L Prelesnik, Elias Nakouzi, Shuai Zhang, James J De Yoreo, Jim Pfaendtner, F Akif Tezcan, Christopher J Mundy
Discrete Orientations of Interfacial Waters Direct Crystallization of Mica-Binding Proteins. The journal of physical chemistry letters 14 (1) (2022)
Robert G Alberstein, Jesse L Prelesnik, Elias Nakouzi, Shuai Zhang, James J De Yoreo, Jim Pfaendtner, F Akif Tezcan, Christopher J Mundy
Discrete Orientations of Interfacial Waters Direct Crystallization of Mica-Binding Proteins. The journal of physical chemistry letters 14 (1) (2022)
Mingfei Zhao, Kacper J Lachowski, Shuai Zhang, Sarah Alamdari, Janani Sampath, Peng Mu, Christopher J Mundy, Jim Pfaendtner, James J De Yoreo, Chun-Long Chen, Lilo D Pozzo, Andrew L Ferguson
Hierarchical Self-Assembly Pathways of Peptoid Helices and Sheets. Biomacromolecules 23 (3) (2022)
Tucker Burgin, Jim Pfaendtner, David A C Beck
Quick and Accurate Estimates of Mutation Effects on Transition-State Stabilization of Enzymes from Molecular Simulations with Restrained Transition States. The journal of physical chemistry. B 126 (48) (2022)
Robert G Alberstein, Jesse L Prelesnik, Elias Nakouzi, Shuai Zhang, James J De Yoreo, Jim Pfaendtner, F Akif Tezcan, Christopher J Mundy
Discrete Orientations of Interfacial Waters Direct Crystallization of Mica-Binding Proteins. The journal of physical chemistry letters (2022)
Sabiha Rustam, Malachi Schram, Zexi Lu, Anne M Chaka, W Steven Rosenthal, Jim Pfaendtner
Optimization of Thermal Conductance at Interfaces Using Machine Learning Algorithms. ACS applied materials & interfaces 14 (28) (2022)
Xin Qi, Yundi Zhao, Kacper J Lachowski, Julia Boese, Yifeng Cai, Orion Dollar, Brittney Hellner, Lilo D Pozzo, Jim Pfaendtner, Jaehun Chun, François Baneyx, Christopher J Mundy
Predictive Theoretical Framework for Dynamic Control of Bioinspired Hybrid Nanoparticle Self-Assembly. ACS nano 16 (2) (2022)
Xin Qi, Biao Jin, Jinhua Zhan, Feng Yan, James J De Yoreo, Chun-Long Chen, Jim Pfaendtner
Molecular Driving Force for Facet Selectivity of Sequence-Defined Amphiphilic Peptoids at Au-Water Interfaces. The journal of physical chemistry. B 126 (27) (2022)
Stephanie R Hare, Jim Pfaendtner
Elucidating the role of catalytic amino acid residues in the peptide-mediated silica oligomerization reaction mechanism. Physical chemistry chemical physics : PCCP 24 (6) (2022)
Kris Strunge, Nina Hoinkis, Helmut Lutz, Sarah Alamdari, Steven J Roeters, Hao Lu, Jim Pfaendtner, Tobias Weidner
Peptide Mimic of the Marine Sponge Protein Silicatein Fabricates Ultrathin Nanosheets of Silicon Dioxide and Titanium Dioxide. Langmuir : the ACS journal of surfaces and colloids 38 (26) (2022)
Li Shao, Jinrong Ma, Jesse L Prelesnik, Yicheng Zhou, Mary Nguyen, Mingfei Zhao, Samson A Jenekhe, Sergei V Kalinin, Andrew L Ferguson, Jim Pfaendtner, Christopher J Mundy, James J De Yoreo, François Baneyx, Chun-Long Chen
Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction. Chemical reviews (2022)
L Schmüser, M Trefz, S J Roeters, W Beckner, Jim Pfaendtner, Daniel Erik Otzen, Sander Woutersen, Mischa Bonn, Dirk Schneider, Tobias Weidner
Membrane Structure of Aquaporin Observed with Combined Experimental and Theoretical Sum Frequency Generation Spectroscopy. Langmuir : the ACS journal of surfaces and colloids 37 (45) (2021)
Orion Dollar, Nisarg Joshi, David A C Beck, Jim Pfaendtner
Attention-based generative models for de novo molecular design. Chemical science 12 (24) (2021)
Jesse L Prelesnik, Robert G Alberstein, Shuai Zhang, Harley Pyles, Julien S Baker, Jim Pfaendtner, James J De Yoreo, F Akif Tezcan, Richard C Remsing, Christopher J Mundy
Ion-dependent protein-surface interactions from intrinsic solvent response. Proceedings of the National Academy of Sciences of the United States of America 118 (26) (2021)
James Ludwig, Josh Smith, Jim Pfaendtner
Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum Albumin. The journal of physical chemistry. B 125 (11) (2021)
Steven J Roeters, Thaddeus W Golbek, Mikkel Bregnhøj, Taner Drace, Sarah Alamdari, Winfried Roseboom, Gertjan Kramer, Tina Šantl-Temkiv, Kai Finster, Jim Pfaendtner, Sander Woutersen, Thomas Boesen, Tobias Weidner
Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water. Nature communications 12 (1) (2021)
Andrew L Ferguson, Johannes Hachmann, Thomas F Miller Iii, Jim Pfaendtner
The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry. The journal of physical chemistry. B 124 (44) (2021)
Nadia N Intan, Jim Pfaendtner
Effect of Fluoroethylene Carbonate Additives on the Initial Formation of the Solid Electrolyte Interphase on an Oxygen-Functionalized Graphitic Anode in Lithium-Ion Batteries. ACS applied materials & interfaces 13 (7) (2021)
Kayla Sprenger, Steven J Roeters, Sergio Mauri, Rolf Mertig, Yoshiharu Nishiyama, Jim Pfaendtner, Tobias Weidner
Direct Evidence for Aligned Binding of Cellulase Enzymes to Cellulose Surfaces. The journal of physical chemistry letters 12 (43) (2021)
Andrew L Ferguson, Johannes Hachmann, Thomas F Miller Iii, Jim Pfaendtner
The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry. The journal of physical chemistry. A 124 (44) (2021)
Mingfei Zhao, Janani Sampath, Sarah Alamdari, Gillian Shen, Chun-Long Chen, Christopher J Mundy, Jim Pfaendtner, Andrew L Ferguson
MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids. The journal of physical chemistry. B 124 (36) (2020)
Maxim Ziatdinov, Shuai Zhang, Orion Dollar, Jim Pfaendtner, Christopher J Mundy, Xin Li, Harley Pyles, David Baker, James J De Yoreo, Sergei V Kalinin
Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data. Nano letters 21 (1) (2020)
Brittney Hellner, Sarah Alamdari, Harley Pyles, Shuai Zhang, Arushi Prakash, Kayla G Sprenger, James J De Yoreo, David Baker, Jim Pfaendtner, François Baneyx
Sequence-Structure-Binding Relationships Reveal Adhesion Behavior of the Car9 Solid-Binding Peptide: An Integrated Experimental and Simulation Study. Journal of the American Chemical Society 142 (5) (2020)
Mengjun Xue, Janani Sampath, Rachel N Gebhart, Håvard Jostein Haugen, S Petter Lyngstadaas, Jim Pfaendtner, Gary P Drobny
Studies of Dynamic Binding of Amino Acids to TiO2 Nanoparticle Surfaces by Solution NMR and Molecular Dynamics Simulations. Langmuir : the ACS journal of surfaces and colloids 36 (35) (2020)
Wesley Beckner, Chowdhury Ashraf, James Lee, David A C Beck, Jim Pfaendtner
Continuous Molecular Representations of Ionic Liquids. The journal of physical chemistry. B 124 (38) (2020)
Sarah Alamdari, Steven J Roeters, Thaddeus W Golbek, Lars Schmüser, Tobias Weidner, Jim Pfaendtner
Orientation and Conformation of Proteins at the Air-Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy. Langmuir : the ACS journal of surfaces and colloids 36 (40) (2020)
Josh Smith, Jim Pfaendtner
Elucidating the Molecular Interactions between Uremic Toxins and the Sudlow II Binding Site of Human Serum Albumin. The journal of physical chemistry. B 124 (19) (2020)
Erika L Buckle, Arushi Prakash, Massimiliano Bonomi, Janani Sampath, Jim Pfaendtner, Gary P Drobny
Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces. Journal of the American Chemical Society 141 (5) (2019)
Prashant S Emani, Yeneneh Y Yimer, Stephen K Davidowski, Rachel N Gebhart, Helen E Ferreira, Ilya Kuprov, Jim Pfaendtner, Gary P Drobny
Combining Molecular and Spin Dynamics Simulations with Solid-State NMR: A Case Study of Amphiphilic Lysine-Leucine Repeat Peptide Aggregates. The journal of physical chemistry. B 123 (51) (2019)
Josh Smith, Patrick McMullen, Zhefan Yuan, Jim Pfaendtner, Shaoyi Jiang
Elucidating Molecular Design Principles for Charge-Alternating Peptides. Biomacromolecules 21 (2) (2019)
Christopher D Fu, Yi He, Jim Pfaendtner
Diagnosing the Impact of External Electric Fields Chemical Kinetics: Application to Toluene Oxidation and Pyrolysis. The journal of physical chemistry. A 123 (14) (2019)
Coco M Mao, Janani Sampath, K G Sprenger, Gary P Drobny, Jim Pfaendtner
Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces. Langmuir : the ACS journal of surfaces and colloids 35 (17) (2019)
Bowen Li, Priyesh Jain, Jinrong Ma, Josh K Smith, Zhefan Yuan, Hsiang-Chieh Hung, Yuwei He, Xiaojie Lin, Kan Wu, Jim Pfaendtner, Shaoyi Jiang
Trimethylamine N-oxide-derived zwitterionic polymers: A new class of ultralow fouling bioinspired materials. Science advances 5 (6) (2019)
Wesley Beckner, Jim Pfaendtner
Fantastic Liquids and Where To Find Them: Optimizations of Discrete Chemical Space. Journal of chemical information and modeling 59 (6) (2019)
Arushi Prakash, Marcel D Baer, Christopher J Mundy, Jim Pfaendtner
Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation. Biomacromolecules 19 (3) (2018)
Amirhossein Mafi, Srinivas Abbina, Manu Thomas Kalathottukaren, James H Morrissey, Charles Haynes, Jayachandran N Kizhakkedathu, Jim Pfaendtner, Keng C Chou
Design of Polyphosphate Inhibitors: A Molecular Dynamics Investigation on Polyethylene Glycol-Linked Cationic Binding Groups. Biomacromolecules 19 (4) (2018)
Christopher D Fu, Jim Pfaendtner
Lifting the Curse of Dimensionality on Enhanced Sampling of Reaction Networks with Parallel Bias Metadynamics. Journal of chemical theory and computation 14 (5) (2018)
Luiz F L Oliveira, Christopher D Fu, Jim Pfaendtner
Density functional tight-binding and infrequent metadynamics can capture entropic effects in intramolecular hydrogen transfer reactions. The Journal of chemical physics 148 (15) (2018)
Arushi Prakash, Christopher D Fu, Massimiliano Bonomi, Jim Pfaendtner
Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics. Journal of chemical theory and computation 14 (10) (2018)
Karl R Oleson, Kayla G Sprenger, Jim Pfaendtner, Daniel T Schwartz
Inhibition of the Exoglucanase Cel7A by a Douglas-Fir-Condensed Tannin. The journal of physical chemistry. B 122 (37) (2018)
Samantha R Summers, K G Sprenger, Jim Pfaendtner, Jan Marchant, Michael F Summers, Joel L Kaar
Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids. The journal of physical chemistry. B 121 (48) (2017)
Josh K Smith, Shaoyi Jiang, Jim Pfaendtner
Redefining the Protein-Protein Interface: Coarse Graining and Combinatorics for an Improved Understanding of Amino Acid Contributions to the Protein-Protein Binding Affinity. Langmuir : the ACS journal of surfaces and colloids 33 (42) (2017)
K G Sprenger, Arushi Prakash, Gary P Drobny, Jim Pfaendtner
Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations. Langmuir : the ACS journal of surfaces and colloids 34 (3) (2017)
Christopher D Fu, Luiz F L Oliveira, Jim Pfaendtner
Assessing Generic Collective Variables for Determining Reaction Rates in Metadynamics Simulations. Journal of chemical theory and computation 13 (3) (2017)