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Journal Articles

A fuzzy classification framework to identify equivalent atoms in complex materials and molecules

King Chun Lai, Sebastian Matera, Christoph Scheurer, Karsten Reuter
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 024129 (2023)
https://doi.org/10.1063/5.0160369
Published: July 2023
View article titled, A fuzzy classification framework to identify equivalent atoms in complex materials and molecules
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Includes: Supplementary data
Journal Articles

Topological Data analysis of Ion Migration Mechanism

Ryuhei Sato, Kazuto Akagi, Shigeyuki Takagi, Kartik Sau, Kazuaki Kisu, Hao Li, Shin-ichi Orimo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 144116 (2023)
https://doi.org/10.1063/5.0143387
Published: April 2023
View article titled, Topological Data analysis of Ion Migration Mechanism
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Includes: Supplementary data
Journal Articles

Locating dynamic contributions to allostery via determining rates of vibrational energy transfer

Humanath Poudel, David M. Leitner
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 015101 (2023)
https://doi.org/10.1063/5.0132089
Published: January 2023
View article titled, Locating dynamic contributions to allostery via determining rates of vibrational energy transfer
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Includes: Supplementary data
Journal Articles

A modernized view of coherence pathways applied to magnetic resonance experiments in unstable, inhomogeneous fields

Editor’s Pick
Alec A. Beaton, Alexandria Guinness, John M. Franck
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 174204 (2022)
https://doi.org/10.1063/5.0105388
Published: November 2022
View article titled, A modernized view of coherence pathways applied to magnetic resonance experiments in unstable, inhomogeneous fields
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Includes: Supplementary data
Journal Articles

Systematic control of collective variables learned from variational autoencoders

Jacob I. Monroe, Vincent K. Shen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 094116 (2022)
https://doi.org/10.1063/5.0105120
Published: September 2022
View article titled, Systematic control of collective variables learned from variational autoencoders
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Includes: Supplementary data
Journal Articles

The many-body electronic interactions of Fe(II)–porphyrin

A. E. Rask, P. M. Zimmerman
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 094110 (2022)
https://doi.org/10.1063/5.0079310
Published: March 2022
View article titled, The many-body electronic interactions of Fe(II)–porphyrin
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Includes: Supplementary data
Journal Articles

Correlation between plastic rearrangements and local structure in a cyclically driven glass

Saheli Mitra, Susana Marín-Aguilar, Srikanth Sastry, Frank Smallenburg, Giuseppe Foffi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 074503 (2022)
https://doi.org/10.1063/5.0077851
Published: February 2022
View article titled, Correlation between plastic rearrangements and local structure in a cyclically driven glass
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Journal Articles

Aqueous choline amino acid deep eutectic solvents

Shurui Miao, Haihui Joy Jiang, Silvia Imberti, Rob Atkin, Gregory Warr
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 214504 (2021)
https://doi.org/10.1063/5.0052479
Published: June 2021
View article titled, Aqueous choline amino acid deep eutectic solvents
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Includes: Supplementary data
Journal Articles

First-principle study of the structures, growth pattern, and properties of (Pt3Cu)n, n = 1–9, clusters

Carlos Daniel Galindo-Uribe, Patrizia Calaminici, Heriberto Cruz-Martínez, Domingo Cruz-Olvera, Omar Solorza-Feria
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 154302 (2021)
https://doi.org/10.1063/5.0045203
Published: April 2021
View article titled, First-principle study of the structures, growth pattern, and properties of (Pt<sub>3</sub>Cu)<sub><em>n</em></sub>, n = 1–9, clusters
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Journal Articles

Assessing the sequence dependence of pyrimidine–pyrimidone (6–4) photoproduct in a duplex double-stranded DNA: A pitfall for microsecond range simulation

Natacha Gillet, Alessio Bartocci, Elise Dumont
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 135103 (2021)
https://doi.org/10.1063/5.0041332
Published: April 2021
View article titled, Assessing the sequence dependence of pyrimidine–pyrimidone (6–4) photoproduct in a duplex double-stranded DNA: A pitfall for microsecond range simulation
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Includes: Supplementary data
Journal Articles

A critical perspective on Markov state model treatments of protein–protein association using coarse-grained simulations

Ziwei He, Fabian Paul, Benoît Roux
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 084101 (2021)
https://doi.org/10.1063/5.0039144
Published: February 2021
View article titled, A critical perspective on Markov state model treatments of protein–protein association using coarse-grained simulations
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Includes: Supplementary data
Journal Articles

Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy

R. Gregor Weiß, Benjamin Ries, Shuzhe Wang, Sereina Riniker
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 084106 (2021)
https://doi.org/10.1063/5.0025797
Published: February 2021
View article titled, Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy
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Journal Articles

High-throughput design of Peierls and charge density wave phases in Q1D organometallic materials

Prakriti Kayastha, Raghunathan Ramakrishnan
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 061102 (2021)
https://doi.org/10.1063/5.0041717
Published: February 2021
View article titled, High-throughput design of Peierls and charge density wave phases in Q1D organometallic materials
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Includes: Supplementary data
Journal Articles

Doubly resonant SFG and DFG spectroscopies: An analytic model for data analysis including distorted and rotated vibronic levels. I. Theory

Bertrand Busson
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 174701 (2020)
https://doi.org/10.1063/5.0022760
Published: November 2020
View article titled, Doubly resonant SFG and DFG spectroscopies: An analytic model for data analysis including distorted and rotated vibronic levels. I. Theory
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Includes: Supplementary data
Journal Articles

Doubly resonant SFG and DFG spectroscopies: An analytic model for data analysis including distorted and rotated vibronic levels. II. Applications

Bertrand Busson
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 174702 (2020)
https://doi.org/10.1063/5.0022761
Published: November 2020
View article titled, Doubly resonant SFG and DFG spectroscopies: An analytic model for data analysis including distorted and rotated vibronic levels. II. Applications
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Includes: Supplementary data
Journal Articles

Heuristics for chemical species identification in dense systems

Betsy M. Rice, William D. Mattson, James P. Larentzos, Edward F. C. Byrd
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 064102 (2020)
https://doi.org/10.1063/5.0015664
Published: August 2020
View article titled, Heuristics for chemical species identification in dense systems
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Includes: Supplementary data
Journal Articles

Photo-excited charge carrier imaging by time-resolved pattern illumination phase microscopy

Kenji Katayama
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 054201 (2020)
https://doi.org/10.1063/5.0009312
Published: August 2020
View article titled, Photo-excited charge carrier imaging by time-resolved pattern illumination phase microscopy
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Includes: Supplementary data
Journal Articles

Photobleaching statistics in single-molecule on-/off-time distributions

Haw Yang, Hao Li, Tao Liu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 151, 174101 (2019)
https://doi.org/10.1063/1.5126500
Published: November 2019
View article titled, Photobleaching statistics in single-molecule on-/off-time distributions
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Journal Articles

Vitrification and nanocrystallization of pure liquid Ni studied using molecular-dynamics simulation

D. V. Louzguine-Luzgin, M. Miyama, K. Nishio, A. A. Tsarkov, A. L. Greer
Journal: The Journal of Chemical Physics
J. Chem. Phys. 151, 124502 (2019)
https://doi.org/10.1063/1.5119307
Published: September 2019
View article titled, Vitrification and nanocrystallization of pure liquid Ni studied using molecular-dynamics simulation
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Journal Articles

Insights on heterogeneity in blinking mechanisms and non-ergodicity using sub-ensemble statistical analysis of single quantum-dots

Amitrajit Mukherjee, Korak Kumar Ray, Chinmay Phadnis, Arunasish Layek, Soumya Bera, Arindam Chowdhury
Journal: The Journal of Chemical Physics
J. Chem. Phys. 151, 084701 (2019)
https://doi.org/10.1063/1.5095870
Published: August 2019
View article titled, Insights on heterogeneity in blinking mechanisms and non-ergodicity using sub-ensemble statistical analysis of single quantum-dots
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Includes: Supplementary data