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Journal Articles

Thermodynamics for reduced models of polymer aggregation based on maximum entropy principle

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Xinyu Zhang, Haiyang Jia, Wuyue Yang, Liangrong Peng, Liu Hong
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 164901 (2025)
https://doi.org/10.1063/5.0252088
Published: April 2025
View articletitled, Thermodynamics for reduced models of polymer aggregation based on maximum entropy principle
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Journal Articles

Suppressing sidechain modes and improving structural resolution for 2D IR spectroscopy via vibrational lifetimes

Open Access
Kayla A. Hess, Cade K. Rohler, Dalton R. Boutwell, Jason M. Snyder, Lauren E. Buchanan
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 054201 (2024)
https://doi.org/10.1063/5.0207523
Published: August 2024
View articletitled, Suppressing sidechain modes and improving structural resolution for 2D IR spectroscopy via vibrational lifetimes
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Journal Articles

Effect of caffeine on the aggregation of amyloid-β–A 3D RISM study

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Priya Dey, Parbati Biswas
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 125101 (2024)
https://doi.org/10.1063/5.0202636
Published: March 2024
View articletitled, Effect of caffeine on the aggregation of amyloid-β–A 3D RISM study
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Includes: Supplementary data
Journal Articles

Variance and higher moments in the sigmoidal self-assembly of branched fibrils

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Mohammadhosein Razbin, Panayotis Benetatos
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 114109 (2024)
https://doi.org/10.1063/5.0190768
Published: March 2024
View articletitled, Variance and higher moments in the sigmoidal self-assembly of branched fibrils
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Journal Articles

Emerging experimental methods to study the thermodynamics of biomolecular condensate formation

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Soumik Ray, Alexander K. Buell
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 091001 (2024)
https://doi.org/10.1063/5.0190160
Published: March 2024
View articletitled, Emerging experimental methods to study the thermodynamics of biomolecular condensate formation
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Journal Articles

Celebrating 25 years of 2D IR spectroscopy

Free
Carlos Baiz, Jens Bredenbeck, Minhaeng Cho, Thomas Jansen, Amber Krummel, Sean Roberts
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 010401 (2024)
https://doi.org/10.1063/5.0190809
Published: January 2024
View articletitled, Celebrating 25 years of 2D IR spectroscopy
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Journal Articles

Coexistence of two coacervate phases of polyglycine in water suggested by polymer reference interaction site model theory

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Tsuyoshi Yamaguchi, Song-Ho Chong, Norio Yoshida
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 245101 (2023)
https://doi.org/10.1063/5.0185157
Published: December 2023
View articletitled, Coexistence of two coacervate phases of polyglycine in water suggested by polymer reference interaction site model theory
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Includes: Supplementary data
Journal Articles

Toward determining amyloid fibril structures using experimental constraints from Raman spectroscopy

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Madeline Harper, Uma Nudurupati, Riley J. Workman, Taras I. Lakoba, Nicholas Perez, Delaney Nelson, Yangguang Ou, David Punihaole
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 225101 (2023)
https://doi.org/10.1063/5.0177437
Published: December 2023
View articletitled, Toward determining amyloid fibril structures using experimental constraints from Raman spectroscopy
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Includes: Supplementary data
Journal Articles

SARS-COV-2 spike protein fragment eases amyloidogenesis of α-synuclein

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Andrew D. Chesney, Buddhadev Maiti, Ulrich H. E. Hansmann
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 015103 (2023)
https://doi.org/10.1063/5.0157331
Published: July 2023
View articletitled, SARS-COV-2 spike protein fragment eases amyloidogenesis of α-synuclein
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Includes: Supplementary data
Journal Articles

Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations

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Phuong H. Nguyen, Philippe Derreumaux
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 235101 (2023)
https://doi.org/10.1063/5.0149419
Published: June 2023
View articletitled, Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations
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Journal Articles

Relaxation dynamics measure the aggregation propensity of amyloid-β and its mutants

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Priya Dey, Parbati Biswas
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 105101 (2023)
https://doi.org/10.1063/5.0138189
Published: March 2023
View articletitled, Relaxation dynamics measure the aggregation propensity of amyloid-β and its mutants
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Includes: Supplementary data
Journal Articles

Determining the impact of gold nanoparticles on amyloid aggregation with 2D IR spectroscopy

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Kayla A. Hess, Nathan J. Spear, Sophia A. Vogelsang, Janet E. Macdonald, Lauren E. Buchanan
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 091101 (2023)
https://doi.org/10.1063/5.0136376
Published: March 2023
View articletitled, Determining the impact of gold nanoparticles on amyloid aggregation with 2D IR spectroscopy
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Includes: Supplementary data
Journal Articles

Essential collective dynamics analysis reveals nonlocal interactions of alpha-synuclein38-95 monomers with fibrillar seeds

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Min Wu, Holger Wille, Maria Stepanova
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 235101 (2022)
https://doi.org/10.1063/5.0116032
Published: December 2022
View articletitled, Essential collective dynamics analysis reveals nonlocal interactions of alpha-synuclein38-95 monomers with fibrillar seeds
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Includes: Supplementary data
Journal Articles

Impact of A2T and D23N mutations on C99 homodimer conformations

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Yan Lu, Freddie R. Salsbury, Jr., Philippe Derreumaux
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 085102 (2022)
https://doi.org/10.1063/5.0101622
Published: August 2022
View articletitled, Impact of A2T and D23N mutations on C99 homodimer conformations
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Includes: Supplementary data
Journal Articles

Protein aggregation rate depends on mechanical stability of fibrillar structure

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Tran Thi Minh Thu, Mai Suan Li
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 055101 (2022)
https://doi.org/10.1063/5.0088689
Published: August 2022
View articletitled, Protein aggregation rate depends on mechanical stability of fibrillar structure
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Journal Articles

Kinetic profiling of therapeutic strategies for inhibiting the formation of amyloid oligomers

Open Access
Thomas C. T. Michaels, Alexander J. Dear, Samuel I. A. Cohen, Michele Vendruscolo, Tuomas P. J. Knowles
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 164904 (2022)
https://doi.org/10.1063/5.0077609
Published: April 2022
View articletitled, Kinetic profiling of therapeutic strategies for inhibiting the formation of amyloid oligomers
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Journal Articles

Publisher’s Note: “Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid- β fragments” [J. Chem. Phys. 156, 084109 (2022)]

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Daiki Fukuhara, Satoru G. Itoh, Hisashi Okumura
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 119901 (2022)
https://doi.org/10.1063/5.0089417
Published: March 2022
View articletitled, Publisher’s Note: “Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid- β fragments” [J. Chem. Phys. 156, 084109 (2022)]
Open the PDF for Publisher’s Note: “Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid- β fragments” [J. Chem. Phys. 156, 084109 (2022)] in another window
Journal Articles

Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments

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Daiki Fukuhara, Satoru G. Itoh, Hisashi Okumura
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 084109 (2022)
https://doi.org/10.1063/5.0081686
Published: February 2022
View articletitled, Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments
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Journal Articles

Distinguishing islet amyloid polypeptide fibril structures with infrared isotope-label spectroscopy

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Vishesh Saxena, Ruben Steendam, Thomas L. C. Jansen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 055101 (2022)
https://doi.org/10.1063/5.0082322
Published: February 2022
View articletitled, Distinguishing islet amyloid polypeptide fibril structures with infrared isotope-label spectroscopy
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Journal Articles

A theoretical analysis of coherent cross-peaks in polarization selective 2DIR for detection of cross-α fibrils

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Dean N. Edun, Olivia M. Cracchiolo, Arnaldo L. Serrano
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 035102 (2022)
https://doi.org/10.1063/5.0070553
Published: January 2022
View articletitled, A theoretical analysis of coherent cross-peaks in polarization selective 2DIR for detection of cross-α fibrils
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