Publications by authors named "KF Freed"

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Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein-Protein Complexes.
Nabil F Faruk, Xiangda Peng, Karl F Freed, Benoît Roux, Tobin R Sosnick

J Chem Theory Comput· March 2022

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Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.
Xiangda Peng, Michael Baxa, Nabil Faruk, Joseph R Sachleben, Sebastian Pintscher, Karl F Freed

J Chem Theory Comput· January 2022

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Molecular dynamics study of water channels in natural and synthetic amyloid-β fibrils.
S R Natesh, A R Hummels, J R Sachleben, T R Sosnick, K F Freed

J Chem Phys· June 2021

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On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations.
Zongan Wang, John M Jumper, Karl F Freed, Tobin R Sosnick

Biophys J· October 2019

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Lattice theory for binding of linear polymers to a solid substrate from polymer melts: I. Influence of chain connectivity on molecular binding and adsorption.
Jacek Dudowicz, Jack F Douglas, Karl F Freed

J Chem Phys· September 2019

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Lattice theory for binding of linear polymers to a solid substrate from polymer melts. II. Influence of van der Waals interactions and chain semiflexibility on molecular binding and adsorption.
Jacek Dudowicz, Jack F Douglas, Karl F Freed

J Chem Phys· September 2019

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Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.
John M Jumper, Nabil F Faruk, Karl F Freed, Tobin R Sosnick

PLoS Comput Biol· December 2018

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Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.
John M Jumper, Nabil F Faruk, Karl F Freed, Tobin R Sosnick

PLoS Comput Biol· December 2018

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A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.
Zongan Wang, John M Jumper, Sheng Wang, Karl F Freed, Tobin R Sosnick

Biophys J· November 2018

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Dielectric virial expansion of polarizable dipolar spheres.
Huada Lian, Jian Qin, Karl F Freed

J Chem Phys· October 2018

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Response to Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".
Joshua A Riback, Micayla A Bowman, Adam Zmyslowski, Catherine R Knoverek, John Jumper, Karl F Freed

Science· August 2018

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Lattice theory of competitive binding: Influence of van der Waals interactions on molecular binding and adsorption to a solid substrate from binary liquid mixtures.
Jacek Dudowicz, Jack F Douglas, Karl F Freed

J Chem Phys· July 2018

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Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.
Joshua A Riback, Micayla A Bowman, Adam M Zmyslowski, Catherine R Knoverek, John M Jumper, Karl F Freed

Science· October 2017

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Mixtures of two self- and mutually-associating liquids: Phase behavior, second virial coefficients, and entropy-enthalpy compensation in the free energy of mixing.
Jacek Dudowicz, Jack F Douglas, Karl F Freed

J Chem Phys· August 2017

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Image method for electrostatic energy of polarizable dipolar spheres.
Kyle S Gustafson, Guoxi Xu, Karl F Freed, Jian Qin

J Chem Phys· August 2017

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Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles.
Esmael J Haddadian, Hao Zhang, Karl F Freed, Jack F Douglas

Sci Rep· February 2017

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Stringlike Cooperative Motion Explains the Influence of Pressure on Relaxation in a Model Glass-Forming Polymer Melt.
Wen-Sheng Xu, Jack F Douglas, Karl F Freed

ACS Macro Lett· December 2016

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Generalized entropy theory of glass-formation in fully flexible polymer melts.
Wen-Sheng Xu, Jack F Douglas, Karl F Freed

J Chem Phys· December 2016

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Image method for induced surface charge from many-body system of dielectric spheres.
Jian Qin, Juan J de Pablo, Karl F Freed

J Chem Phys· September 2016

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Erratum: "Ionic strength independence of charge distributions in solvation of biomolecules" [J. Chem. Phys. 141, 22D503 (2014)].
J J Virtanen, T R Sosnick, K F Freed

J Chem Phys· August 2016

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Relation Between Solvent Quality and Phase Behavior of Ternary Mixtures of Polymers and Two Solvents that Exhibit Cononsolvency.
Jacek Dudowicz, Karl F Freed, Jack F Douglas

J Phys Chem B· June 2016

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Self-assembly and glass-formation in a lattice model of telechelic polymer melts: Influence of stiffness of the sticky bonds.
Wen-Sheng Xu, Karl F Freed

J Chem Phys· June 2016

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A theory of interactions between polarizable dielectric spheres.
Jian Qin, Jiyuan Li, Victor Lee, Heinrich Jaeger, Juan J de Pablo, Karl F Freed

J Colloid Interface Sci· May 2016

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Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.
Wookyung Yu, Michael C Baxa, Isabelle Gagnon, Karl F Freed, Tobin R Sosnick

Proc Natl Acad Sci U S A· April 2016

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Phase behavior and second osmotic virial coefficient for competitive polymer solvation in mixed solvent solutions.
Jacek Dudowicz, Karl F Freed, Jack F Douglas

J Chem Phys· November 2015

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