Jim Pfaendtner

发表

Probing How Defects in Self-assembled Monolayers Affect Peptide Adsorption with Molecular Simulation

K. G. Sprenger, Yi He, Jim Pfaendtner, 2015, FOMMS.

Unit Operations Lab Bazaar

Jim Pfaendtner, Michael E. Prudich, Daina Briedis, 2011 .

Data science: Accelerating innovation and discovery in chemical engineering

James M. Carothers, Jim Pfaendtner, Venkat R. Subramanian, 2016 .

Fantastic Liquids and Where To Find Them: Optimizations of Discrete Chemical Space

Jim Pfaendtner, Wesley Beckner, J. Pfaendtner, 2019, J. Chem. Inf. Model..

A New Graduate-Level Seminar to Prepare Students for the Next Step in Their Careers.

Jim Pfaendtner, Kelly L. Fleming, James F. Matthaei, 2015 .

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble.

Massimiliano Bonomi, Jim Pfaendtner, Michael Deighan, 2012, Journal of chemical theory and computation.

Metadynamics to Enhance Sampling in Biomolecular Simulations.

Jim Pfaendtner, J. Pfaendtner, 2019, Methods in molecular biology.

Promoting transparency and reproducibility in enhanced molecular simulations

Jakub Rydzewski, Toni Giorgino, Massimiliano Bonomi, 2019, Nature Methods.

Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data.

Jim Pfaendtner, Maxim Ziatdinov, David Baker, 2020, Nano letters.

Topical Plenary: Topical Conference in Molecular and Materials Data Science (Invited Talks)

Jim Pfaendtner, Elizabeth Nance, Johannes Hachmann, 2019 .

Forum Plenary: Computational Molecular Science and Engineering Forum (Invited Talks)

Jim Pfaendtner, Sapna Sarupria, 2019 .

The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry.

Jim Pfaendtner, Andrew L. Ferguson, Thomas F. Miller, 2020, The journal of physical chemistry. B.

IL-Net: Using Expert Knowledge to Guide the Design of Furcated Neural Networks

Jim Pfaendtner, Garrett B. Goh, Wesley Beckner, 2018, 2018 IEEE International Conference on Big Data (Big Data).

Application of machine learning to pyrolysis reaction networks: Reducing model solution time to enable process optimization

Jim Pfaendtner, David A. C. Beck, Daniel T. Schwartz, 2017, Comput. Chem. Eng..

Multimodal Deep Neural Networks using Both Engineered and Learned Representations for Biodegradability Prediction pdf

Abhinav Vishnu, Jim Pfaendtner, Garrett B. Goh, 2018, ArXiv.

Lifting the Curse of Dimensionality on Enhanced Sampling of Reaction Networks with Parallel Bias Metadynamics.

Jim Pfaendtner, Christopher D Fu, 2018, Journal of chemical theory and computation.

Assessing Generic Collective Variables for Determining Reaction Rates in Metadynamics Simulations.

Jim Pfaendtner, Christopher D Fu, Luiz F L Oliveira, 2017, Journal of chemical theory and computation.

Integration of the Chemical Engineering Laboratory with a Focus on Bio-Fuel Production

Jim Pfaendtner, Danilo C. Pozzo, William B. Baratuci, 2011 .

Tackling sampling challenges in biomolecular simulations.

Massimiliano Bonomi, Jim Pfaendtner, Alessandro Barducci, 2015, Methods in molecular biology.

Giving Attention to Generative VAE Models for De Novo Molecular Design

Jim Pfaendtner, Orion Dollar, Nisarg Joshi, 2021 .

Ionic Liquids Can Selectively Change the Conformational Free-Energy Landscape of Sugar Rings.

Jim Pfaendtner, J. Pfaendtner, Zack Jarin, 2014, Journal of chemical theory and computation.

New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations.

Jim Pfaendtner, Pratyush Tiwary, Kelly L. Fleming, 2016, The journal of physical chemistry. A.

Car–Parrinello Molecular Dynamics + Metadynamics Study of High-Temperature Methanol Oxidation Reactions Using Generic Collective Variables

Jim Pfaendtner, Shaohui Zheng, J. Pfaendtner, 2014 .

Determining energy barriers and selectivities of a multi-pathway system with infrequent metadynamics.

Jim Pfaendtner, J. Pfaendtner, Christopher D Fu, 2017, The Journal of chemical physics.

Characterizing the catalyzed hydrolysis of β-1,4 glycosidic bonds using density functional theory.

Jim Pfaendtner, Kelly L. Fleming, J. Pfaendtner, 2013, The journal of physical chemistry. A.

Systematic multiscale parameterization of heterogeneous elastic network models of proteins.

Jim Pfaendtner, Gregory A Voth, Edward Lyman, 2008, Biophysical journal.

Millisecond Pulsed Films Unify the Mechanisms of Cellulose Fragmentation

Jim Pfaendtner, Paul J. Dauenhauer, P. Dauenhauer, 2016 .

Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.

Jim Pfaendtner, Gregory A Voth, G. Voth, 2009, Biophysical journal.

Free energy of solvated salt bridges: a simulation and experimental study.

Jim Pfaendtner, Andrew D White, Qing Shao, 2013, The journal of physical chemistry. B.

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics.

Massimiliano Bonomi, Jim Pfaendtner, M. Bonomi, 2015, Journal of chemical theory and computation.

A systematic methodology for defining coarse-grained sites in large biomolecules.

Jim Pfaendtner, Gregory A Voth, Lanyuan Lu, 2008, Biophysical journal.

Structure and dynamics of the actin filament.

Jim Pfaendtner, Gregory A Voth, Thomas D Pollard, 2010, Journal of molecular biology.

Nucleotide-dependent conformational states of actin

Jim Pfaendtner, Gregory A Voth, Michele Parrinello, 2009, Proceedings of the National Academy of Sciences.

Lexicography of kinetic modeling of complex reaction networks

Jim Pfaendtner, Linda J. Broadbelt, L. Broadbelt, 2005 .

The 1-D hindered rotor approximation

Jim Pfaendtner, Linda J. Broadbelt, L. Broadbelt, 2007 .