Peter G Wolynes

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 81

Top Topics

Molecular Dynamics Simulations

Binding Protein

Amyotrophic Lateral Sclerosis

Single Molecule

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

The journal of physical chemistry. B

Journal of the American Chemical Society

Nature communications

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

Publications

Zhiyu Cao, Peter G Wolynes
Motorized chain models of the ideal chromosome. Proceedings of the National Academy of Sciences of the United States of America 121 (28) (2024)
Ezequiel A Galpern, Hana Jaafari, Carlos Bueno, Peter G Wolynes, Diego U Ferreiro
Reassessing the exon-foldon correspondence using frustration analysis. Proceedings of the National Academy of Sciences of the United States of America 121 (28) (2024)
Xingyue Guan, Qian-Yuan Tang, Weitong Ren, Mingchen Chen, Wei Wang, Peter G Wolynes, Wenfei Li
Predicting protein conformational motions using energetic frustration analysis and AlphaFold2. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Hana Jaafari, Carlos Bueno, Nicholas P Schafer, Jonathan Martin, Faruck Morcos, Peter G Wolynes
The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes. Proceedings of the National Academy of Sciences of the United States of America 121 (21) (2024)
Chenghao Zhang, Sohang Kundu, Nancy Makri, Martin Gruebele, Peter G Wolynes
Quantum information scrambling and chemical reactions. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Ezequiel A Galpern, Hana Jaafari, Carlos Bueno, Peter G Wolynes, Diego U Ferreiro
Reassessing the exon-foldon correspondence using frustration analysis. Proceedings of the National Academy of Sciences of the United States of America 121 (28) (2024)
Chenghao Zhang, Sohang Kundu, Nancy Makri, Martin Gruebele, Peter G Wolynes
Quantum information scrambling and chemical reactions. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Chenghao Zhang, Sohang Kundu, Nancy Makri, Martin Gruebele, Peter G Wolynes
Quantum information scrambling and chemical reactions. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Chenghao Zhang, Sohang Kundu, Nancy Makri, Martin Gruebele, Peter G Wolynes
Quantum information scrambling and chemical reactions. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Hana Jaafari, Carlos Bueno, Nicholas P Schafer, Jonathan Martin, Faruck Morcos, Peter G Wolynes
The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes. Proceedings of the National Academy of Sciences of the United States of America 121 (21) (2024)
Hana Jaafari, Carlos Bueno, Nicholas P Schafer, Jonathan Martin, Faruck Morcos, Peter G Wolynes
The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes. Proceedings of the National Academy of Sciences of the United States of America 121 (21) (2024)
Zhiyu Cao, Peter G Wolynes
Motorized chain models of the ideal chromosome. Proceedings of the National Academy of Sciences of the United States of America 121 (28) (2024)
Zhiyu Cao, Peter G Wolynes
Motorized chain models of the ideal chromosome. Proceedings of the National Academy of Sciences of the United States of America 121 (28) (2024)
Xingyue Guan, Qian-Yuan Tang, Weitong Ren, Mingchen Chen, Wei Wang, Peter G Wolynes, Wenfei Li
Predicting protein conformational motions using energetic frustration analysis and AlphaFold2. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Xingyue Guan, Qian-Yuan Tang, Weitong Ren, Mingchen Chen, Wei Wang, Peter G Wolynes, Wenfei Li
Predicting protein conformational motions using energetic frustration analysis and AlphaFold2. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Ezequiel A Galpern, Hana Jaafari, Carlos Bueno, Peter G Wolynes, Diego U Ferreiro
Reassessing the exon-foldon correspondence using frustration analysis. Proceedings of the National Academy of Sciences of the United States of America 121 (28) (2024)
Hana Jaafari, Carlos Bueno, Nicholas P Schafer, Jonathan Martin, Faruck Morcos, Peter G Wolynes
The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes. Proceedings of the National Academy of Sciences of the United States of America 121 (21) (2024)
Maria I Freiberger, Victoria Ruiz Serra, Camila Pontes, Miguel Romero-Durana, Pablo Galaz-Davison, Cesar A Ramírez-Sarmiento, Claudio David Schuster, Marcelo A Marti, Peter G Wolynes, Diego U Ferreiro, R Gonzalo Parra, Alfonso Valencia
Local energetic frustration conservation in protein families and superfamilies. Nature communications 14 (1) (2023)
Chenghao Zhang, Martin Gruebele, David E Logan, Peter G Wolynes
Surface crossing and energy flow in many-dimensional quantum systems. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Xun Chen, Shikai Jin, Mingchen Chen, Carlos Bueno, Peter G Wolynes
The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Cagla Sahin, Aikaterini Motso, Xinyu Gu, Hannes Feyrer, Dilraj Lama, Tina Arndt, Anna Rising, Genis Valentin Gese, B Martin Hällberg, Erik G Marklund, Nicholas P Schafer, Katja Petzold, Kaare Teilum, Peter G Wolynes, Michael Landreh
Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. Journal of the American Chemical Society 145 (19) (2023)
Chenghao Zhang, Martin Gruebele, David E Logan, Peter G Wolynes
Surface crossing and energy flow in many-dimensional quantum systems. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Xun Chen, Shikai Jin, Mingchen Chen, Carlos Bueno, Peter G Wolynes
The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Xun Chen, Shikai Jin, Mingchen Chen, Carlos Bueno, Peter G Wolynes
The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Cagla Sahin, Aikaterini Motso, Xinyu Gu, Hannes Feyrer, Dilraj Lama, Tina Arndt, Anna Rising, Genis Valentin Gese, B Martin Hällberg, Erik G Marklund, Nicholas P Schafer, Katja Petzold, Kaare Teilum, Peter G Wolynes, Michael Landreh
Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. Journal of the American Chemical Society 145 (19) (2023)
Xun Chen, Shikai Jin, Mingchen Chen, Carlos Bueno, Peter G Wolynes
The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Peter G Wolynes, Martin Gruebele
Quantum scrambling across an energy barrier. Proceedings of the National Academy of Sciences of the United States of America 120 (52) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Peter G Wolynes, Martin Gruebele
Quantum scrambling across an energy barrier. Proceedings of the National Academy of Sciences of the United States of America 120 (52) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Xun Chen, Shikai Jin, Mingchen Chen, Carlos Bueno, Peter G Wolynes
The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Xun Chen, Shikai Jin, Mingchen Chen, Carlos Bueno, Peter G Wolynes
The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Peter G Wolynes, Martin Gruebele
Quantum scrambling across an energy barrier. Proceedings of the National Academy of Sciences of the United States of America 120 (52) (2023)
Chenghao Zhang, Martin Gruebele, David E Logan, Peter G Wolynes
Surface crossing and energy flow in many-dimensional quantum systems. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Maria I Freiberger, Victoria Ruiz Serra, Camila Pontes, Miguel Romero-Durana, Pablo Galaz-Davison, Cesar A Ramírez-Sarmiento, Claudio David Schuster, Marcelo A Marti, Peter G Wolynes, Diego U Ferreiro, R Gonzalo Parra, Alfonso Valencia
Local energetic frustration conservation in protein families and superfamilies. Nature communications 14 (1) (2023)
Xun Chen, Shikai Jin, Mingchen Chen, Carlos Bueno, Peter G Wolynes
The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Cagla Sahin, Aikaterini Motso, Xinyu Gu, Hannes Feyrer, Dilraj Lama, Tina Arndt, Anna Rising, Genis Valentin Gese, B Martin Hällberg, Erik G Marklund, Nicholas P Schafer, Katja Petzold, Kaare Teilum, Peter G Wolynes, Michael Landreh
Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. Journal of the American Chemical Society (2023)
Chenghao Zhang, Martin Gruebele, David E Logan, Peter G Wolynes
Surface crossing and energy flow in many-dimensional quantum systems. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Peter G Wolynes, Martin Gruebele
Quantum scrambling across an energy barrier. Proceedings of the National Academy of Sciences of the United States of America 120 (52) (2023)
Cagla Sahin, Aikaterini Motso, Xinyu Gu, Hannes Feyrer, Dilraj Lama, Tina Arndt, Anna Rising, Genis Valentin Gese, B Martin Hällberg, Erik G Marklund, Nicholas P Schafer, Katja Petzold, Kaare Teilum, Peter G Wolynes, Michael Landreh
Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. Journal of the American Chemical Society 145 (19) (2023)
Vinícius de Godoi Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter G Wolynes, José Nelson Onuchic, Michele Di Pierro
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature communications 14 (1) (2023)
Cagla Sahin, Aikaterini Motso, Xinyu Gu, Hannes Feyrer, Dilraj Lama, Tina Arndt, Anna Rising, Genis Valentin Gese, B Martin Hällberg, Erik G Marklund, Nicholas P Schafer, Katja Petzold, Kaare Teilum, Peter G Wolynes, Michael Landreh
Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. Journal of the American Chemical Society 145 (19) (2023)
Cagla Sahin, Aikaterini Motso, Xinyu Gu, Hannes Feyrer, Dilraj Lama, Tina Arndt, Anna Rising, Genis Valentin Gese, B Martin Hällberg, Erik G Marklund, Nicholas P Schafer, Katja Petzold, Kaare Teilum, Peter G Wolynes, Michael Landreh
Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. Journal of the American Chemical Society 145 (19) (2023)
Xinyu Gu, Nicholas P Schafer, Carlos Bueno, Wei Lu, Peter G Wolynes
A structural dynamics model for how CPEB3 binding to SUMO2 can regulate translational control in dendritic spines. PLoS computational biology 18 (11) (2022)
Xun Chen, Mingchen Chen, Peter G Wolynes
Exploring the Interplay between Disordered and Ordered Oligomer Channels on the Aggregation Energy Landscapes of α-Synuclein. The journal of physical chemistry. B 126 (28) (2022)
Xun Chen, Mingchen Chen, Peter G Wolynes, Pernilla Wittung-Stafshede, Harry B Gray
Frustration Dynamics and Electron-Transfer Reorganization Energies in Wild-Type and Mutant Azurins. Journal of the American Chemical Society 144 (9) (2022)
Xun Chen, Min-Yeh Tsai, Peter G Wolynes
The Role of Charge Density Coupled DNA Bending in Transcription Factor Sequence Binding Specificity: A Generic Mechanism for Indirect Readout. Journal of the American Chemical Society 144 (4) (2022)
Yangyang Zhang, Mingchen Chen, Jiajun Lu, Wenfei Li, Peter G Wolynes, Wei Wang
Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis. The journal of physical chemistry. B 126 (36) (2022)
Shikai Jin, Carlos Bueno, Wei Lu, Qian Wang, Mingchen Chen, Xun Chen, Peter G Wolynes, Yang Gao
Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA. Proceedings of the National Academy of Sciences of the United States of America 119 (32) (2022)
Xun Chen, Wei Lu, Min-Yeh Tsai, Shikai Jin, Peter G Wolynes
Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model. Journal of biological physics 48 (1) (2022)
Murilo Nogueira Sanches, R Gonzalo Parra, Rafael Giordano Viegas, Antonio Bento Oliveira Junior, Peter G Wolynes, Diego U Ferreiro, Ingrid B S Martins
Resolving the fine structure in the energy landscapes of repeat proteins. QRB discovery 3 (2022)
Carlos Bueno, James Liman, Nicholas P Schafer, Margaret S Cheung, Peter G Wolynes
A generalized Flory-Stockmayer kinetic theory of connectivity percolation and rigidity percolation of cytoskeletal networks. PLoS computational biology 18 (5) (2022)
Yuechuan Xu, Kaitlin Knapp, Kyle N Le, Nicholas P Schafer, Mohammad S Safari, Aram Davtyan, Peter G Wolynes, Peter G Vekilov
Frustrated peptide chains at the fibril tip control the kinetics of growth of amyloid-β fibrils. Proceedings of the National Academy of Sciences of the United States of America 118 (38) (2021)
Jia-Liang Shen, Min-Yeh Tsai, Nicholas P Schafer, Peter G Wolynes
Modeling Protein Aggregation Kinetics: The Method of Second Stochasticization. The journal of physical chemistry. B 125 (4) (2021)
Murilo Nogueira Sanches, Kaitlin Knapp, Antonio B Oliveira, Peter G Wolynes, José Nelson Onuchic, Ingrid B S Martins
Examining the Ensembles of Amyloid-β Monomer Variants and Their Propensities to Form Fibers Using an Energy Landscape Visualization Method. The journal of physical chemistry. B 126 (1) (2021)
Xinyu Gu, Nicholas P Schafer, Peter G Wolynes
Vectorial channeling as a mechanism for translational control by functional prions and condensates. Proceedings of the National Academy of Sciences of the United States of America 118 (47) (2021)
Stefano Gianni, María Inés Freiberger, Per Jemth, Diego U Ferreiro, Peter G Wolynes, Monika Fuxreiter
Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly. Accounts of chemical research 54 (5) (2021)
Mark D Ediger, Martin Gruebele, Vassiliy Lubchenko, Peter G Wolynes
Glass Dynamics Deep in the Energy Landscape. The journal of physical chemistry. B 125 (32) (2021)
Maria I Freiberger, Peter G Wolynes, Diego U Ferreiro, Monika Fuxreiter
Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility. The journal of physical chemistry. B 125 (10) (2021)
Wei Chen, Wei Lu, Peter G Wolynes, Elizabeth A Komives
Single-molecule conformational dynamics of a transcription factor reveals a continuum of binding modes controlling association and dissociation. Nucleic acids research 49 (19) (2021)
Wei Lu, Carlos Bueno, Nicholas P Schafer, Joshua Moller, Shikai Jin, Xun Chen, Mingchen Chen, Xinyu Gu, Aram Davtyan, Juan J de Pablo, Peter G Wolynes
OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PLoS computational biology 17 (2) (2021)
Vassiliy Lubchenko, Peter G Wolynes
Photon Activation of Glassy Dynamics: A Mechanism for Photoinduced Fluidization, Aging, and Information Storage in Amorphous Materials. The journal of physical chemistry. B 124 (38) (2020)
Shikai Jin, Mingchen Chen, Xun Chen, Carlos Bueno, Wei Lu, Nicholas P Schafer, Xingcheng Lin, José Nelson Onuchic, Peter G Wolynes
Protein Structure Prediction in CASP13 Using AWSEM-Suite. Journal of chemical theory and computation 16 (6) (2020)
Mingchen Chen, Xun Chen, Nicholas P Schafer, Cecilia Clementi, Elizabeth A Komives, Diego U Ferreiro, Peter G Wolynes
Surveying biomolecular frustration at atomic resolution. Nature communications 11 (1) (2020)
Shikai Jin, Mitchell D Miller, Mingchen Chen, Nicholas P Schafer, Xingcheng Lin, Xun Chen, George N Phillips, Peter G Wolynes
Molecular-replacement phasing using predicted protein structures from AWSEM-Suite. IUCrJ 7 (Pt 6) (2020)
Xun Chen, Mingchen Chen, Nicholas P Schafer, Peter G Wolynes
Exploring the interplay between fibrillization and amorphous aggregation channels on the energy landscapes of tau repeat isoforms. Proceedings of the National Academy of Sciences of the United States of America 117 (8) (2020)
James Liman, Carlos Bueno, Yossi Eliaz, Nicholas P Schafer, M Neal Waxham, Peter G Wolynes, Herbert Levine, Margaret S Cheung
The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks. Proceedings of the National Academy of Sciences of the United States of America 117 (20) (2020)
Xinyu Gu, Nicholas P Schafer, Qian Wang, Sarah S Song, Mingchen Chen, Melvin Neal Waxham, Peter G Wolynes
Exploring the F-actin/CPEB3 interaction and its possible role in the molecular mechanism of long-term memory. Proceedings of the National Academy of Sciences of the United States of America 117 (36) (2020)
Mingchen Chen, Xun Chen, Shikai Jin, Wei Lu, Xingcheng Lin, Peter G Wolynes
Protein Structure Refinement Guided by Atomic Packing Frustration Analysis. The journal of physical chemistry. B 124 (48) (2020)
Maria I Freiberger, A Brenda Guzovsky, Peter G Wolynes, R Gonzalo Parra, Diego U Ferreiro
Local frustration around enzyme active sites. Proceedings of the National Academy of Sciences of the United States of America 116 (10) (2019)
Qian Wang, Mingchen Chen, Nicholas P Schafer, Carlos Bueno, Sarah S Song, Andy Hudmon, Peter G Wolynes, M Neal Waxham, Margaret S Cheung
Assemblies of calcium/calmodulin-dependent kinase II with actin and their dynamic regulation by calmodulin in dendritic spines. Proceedings of the National Academy of Sciences of the United States of America 116 (38) (2019)
Dana Krepel, Aram Davtyan, Nicholas P Schafer, Peter G Wolynes, José N Onuchic
Braiding topology and the energy landscape of chromosome organization proteins. Proceedings of the National Academy of Sciences of the United States of America 117 (3) (2019)
Justin Chen, Nicholas P Schafer, Peter G Wolynes, Cecilia Clementi
Localizing Frustration in Proteins Using All-Atom Energy Functions. The journal of physical chemistry. B 123 (21) (2019)
Min-Yeh Tsai, Weihua Zheng, Mingchen Chen, Peter G Wolynes
Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation. Journal of the American Chemical Society 141 (45) (2019)
Xingcheng Lin, Nicholas P Schafer, Wei Lu, Shikai Jin, Xun Chen, Mingchen Chen, José N Onuchic, Peter G Wolynes
Forging tools for refining predicted protein structures. Proceedings of the National Academy of Sciences of the United States of America 116 (19) (2019)
Yuechuan Xu, Mohammad S Safari, Wenchuan Ma, Nicholas P Schafer, Peter G Wolynes, Peter G Vekilov
Steady, Symmetric, and Reversible Growth and Dissolution of Individual Amyloid-β Fibrils. ACS chemical neuroscience 10 (6) (2019)
Benjamin Schuler, Attila Szabo, Peter G Wolynes
Tribute to William A. Eaton. The journal of physical chemistry. B 122 (49) (2019)
Mingchen Chen, Nicholas P Schafer, Peter G Wolynes
Surveying the Energy Landscapes of Aβ Fibril Polymorphism. The journal of physical chemistry. B 122 (49) (2018)
Mingchen Chen, Xingcheng Lin, Wei Lu, Nicholas P Schafer, José Nelson Onuchic, Peter G Wolynes
Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields. Journal of chemical theory and computation 14 (11) (2018)