Molecular dynamics simulations of cyanine dimers attached to DNA Holliday junctions

Austin Biaggne, Young C. Kim, Joseph. S. Melinger, William B. Knowlton, Bernard Yurke and Lan Li

RSC Adv., 2022, 12, 28063
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Effect of hydrophilicity-imparting substituents on exciton delocalization in squaraine dye aggregates covalently templated to DNA Holliday junctions

Gissela Pascual, Simon K. Roy, German Barcenas, Christopher K. Wilson, Keitel Cervantes-Salguero, Olena M. Obukhova, Alexander I. Krivoshey, Ewald A. Terpetschnig, Anatoliy L. Tatarets, Lan Li, Bernard Yurke, William B. Knowlton, Olga A. Mass, Ryan D. Pensack and Jeunghoon Lee

Nanoscale, 2024, 16, 1206
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Site-specific photo-crosslinking in a double crossover DNA tile facilitated by squaraine dye aggregates: advancing thermally stable and uniform DNA nanostructures

Shibani Basu, Simon K. Roy, Mandeep Sharma, German Barcenas, Bernard Yurke, William B. Knowlton and Jeunghoon Lee

Biomater. Sci., 2025, 13, 1742
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Tunable and robust optical and structural properties of a cooperative squaraine-dye aggregate-DNA DX-DAE tile system

Simon K. Roy, Nolan Olaso, Paul H. Davis, Olga A. Mass, Keitel Cervantes-Salguero, Jeunghoon Lee, Ryan D. Pensack, John A. Hall, Bernard Yurke and William B. Knowlton

Nanoscale, 2025, 17, 18646
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Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

Divita Mathur, Sebastián A. Díaz, Niko Hildebrandt, Ryan D. Pensack, Bernard Yurke, Austin Biaggne, Lan Li, Joseph S. Melinger, Mario G. Ancona, William B. Knowlton and Igor L. Medintz

Chem. Soc. Rev., 2023, 52, 7848
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Oxygenolysis of a series of copper(ii)-flavonolate adducts varying the electronic factors on supporting ligands as a mimic of quercetin 2,4-dioxygenase-like activity

Nirmalya Podder, Subhasis Dey, Anakuthil Anoop and Sukanta Mandal

Dalton Trans., 2022, 51, 4338
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Activating charge-transfer state formation in strongly-coupled dimers using DNA scaffolds

Stephanie M. Hart, James L. Banal, Maria A. Castellanos, Larysa Markova, Yuliia Vyborna, Jeffrey Gorman, Robert Häner, Adam P. Willard, Mark Bathe and Gabriela S. Schlau-Cohen

Chem. Sci., 2022, 13, 13020
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Oblique Packing and Tunable Excitonic Coupling in DNA‐Templated Squaraine Rotaxane Dimer Aggregates

Matthew S. Barclay, Christopher K. Wilson, Simon K. Roy, Olga A. Mass, Olena M. Obukhova, Rostyslav P. Svoiakov, Anatoliy L. Tatarets, Azhad U. Chowdhury, Jonathan S. Huff, Daniel B. Turner, Paul H. Davis, Ewald A. Terpetschnig, Bernard Yurke, William B. Knowlton, Jeunghoon Lee and Ryan D. Pensack

ChemPhotoChem, 2022, 6
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Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

Austin Biaggne, Lawrence Spear, German Barcenas, Maia Ketteridge, Young C. Kim, Joseph S. Melinger, William B. Knowlton, Bernard Yurke and Lan Li

Molecules, 2022, 27, 3456
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Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines

Nicholas D. Wright, Jonathan S. Huff, Matthew S. Barclay, Christopher K. Wilson, German Barcenas, Katelyn M. Duncan, Maia Ketteridge, Olena M. Obukhova, Alexander I. Krivoshey, Anatoliy L. Tatarets, Ewald A. Terpetschnig, Jacob C. Dean, William B. Knowlton, Bernard Yurke, Lan Li, Olga A. Mass, Paul H. Davis, Jeunghoon Lee, Daniel B. Turner and Ryan D. Pensack

J. Phys. Chem. A, 2023, 127, 1141
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Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions

German Barcenas, Austin Biaggne, Olga A. Mass, William B. Knowlton, Bernard Yurke and Lan Li

IJMS, 2023, 24, 4059
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Steric and Electronic Effect in Unsymmetrical Squaraine Dyes for Dye-Sensitized Solar Cells

Indrajeet S. Nawghare, Ambarish Kumar Singh, Ashakiran Maibam, Sailaja Krishnamurty, Kothandam Krishnamoorthy and Jayaraj Nithyanandhan

J. Phys. Chem. C, 2023, 127, 22473
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Computational Calculation of Dissolved Organic Matter Absorption Spectra

Frank Leresche, Elena A. Vialykh and Fernando L. Rosario-Ortiz

Environ. Sci. Technol., 2022, 56, 491
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Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates

Olga A. Mass, Christopher K. Wilson, German Barcenas, Ewald. A. Terpetschnig, Olena M. Obukhova, Olga S. Kolosova, Anatoliy L. Tatarets, Lan Li, Bernard Yurke, William B. Knowlton, Ryan. D. Pensack and Jeunghoon Lee

J. Phys. Chem. C, 2022, 126, 3475
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Electronic Structure and Excited-State Dynamics of DNA-Templated Monomers and Aggregates of Asymmetric Polymethine Dyes

Katelyn M. Duncan, Hannah M. Byers, Madaline E. Houdek, Simon K. Roy, Austin Biaggne, Matthew S. Barclay, Lance K. Patten, Jonathan S. Huff, Donald L. Kellis, Christopher K. Wilson, Jeunghoon Lee, Paul H. Davis, Olga A. Mass, Lan Li, Daniel B. Turner, John A. Hall, William B. Knowlton, Bernard Yurke and Ryan D. Pensack

J. Phys. Chem. A, 2023, 127, 4901
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Singlet Excited-State Lifetimes of Nitro- and Dimethylamino-Substituted Bacteriochlorins Vary in Their Sensitivity to Solvent Polarity

Katelyn M. Duncan, Devan R. Watt, William B. Knowlton, Daniel B. Turner, Olga A. Mass and Ryan D. Pensack

J. Phys. Chem. C, 2025
DOI: 10.1021/acs.jpcc.5c01649

Effect of Substituent Location on the Relationship between the Transition Dipole Moments, Difference Static Dipole, and Hydrophobicity in Squaraine Dyes for Quantum Information Devices

Maia Ketteridge, Austin Biaggne, Ryan Rau, German Barcenas, Olga A. Mass, William B. Knowlton, Bernard Yurke and Lan Li

Molecules, 2023, 28, 2163
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Influence of Substituents on the Vectorial Difference Static Dipole Upon Excitation in Synthetic Bacteriochlorins

Maia N. Ketteridge, Devan R. Watt, Katelyn M. Duncan, German Barcenas, Kaden Shaw, William B. Knowlton, Bernard Yurke, Ryan D. Pensack, Olga A. Mass and Lan Li

J. Phys. Chem. A, 2024, 128, 7581
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(Z)-3-(Dicyanomethylene)-4-((5-fluoro-3,3-dimethyl-1-(3-phenylpropyl)-3H-indol-1-ium-2-yl) methylene)-2-(((E)-5-fluoro-3,3-dimethyl-1-(3-phenylpropyl)indolin-2-ylidene)methyl) cyclobut-1-en-1-olate

Stefanie Casa, Guliz Ersoy Ozmen and Maged Henary

Molbank, 2023, 2023, M1576
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NIR-Sensitive Squaraine Dye—Peptide Conjugate for Trypsin Fluorogenic Detection

Priyanka Balyan, Shekhar Gupta, Sai Kiran Mavileti, Shyam S. Pandey and Tamaki Kato

Biosensors, 2024, 14, 458
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Supramolecular Approach to Tuning the Photophysical Properties of Quadrupolar Squaraines

Anna Kaczmarek-Kȩdziera, Borys Ośmiałowski, Piotr S. Żuchowski and Dariusz Kȩdziera

Front. Chem., 2022, 9
DOI: 10.3389/fchem.2021.800541

Conformational and environmental effects on the electronic and vibrational properties of dyes for solar cell devices

Edoardo Buttarazzi, Antonio Inchingolo, Danilo Pedron, Marta Erminia Alberto, Elisabetta Collini and Alessio Petrone

The Journal of Chemical Physics, 2024, 160
DOI: 10.1063/5.0207770

The Design and Bioimaging Applications of NIR Fluorescent Organic Dyes with High Brightness

Jiaxing Wu, Zhenxiong Shi, Linlin Zhu, Jie Li, Xu Han, Man Xu, Shiping Hao, Yibo Fan, Tao Shao, Hua Bai, Bo Peng, Wenbo Hu, Xiaowang Liu, Chuanhao Yao, Lin Li and Wei Huang

Advanced Optical Materials, 2022, 10
DOI: 10.1002/adom.202102514

Impact of the Acceptor Group on the Properties of Triphenylamine-Donor–Acceptor Dyes: An Experimental and Computational Study

Elkhansa Elbashier, Pawel Wagner, David L. Officer and Keith C. Gordon

J. Phys. Chem. A, 2025, 129, 1026
DOI: 10.1021/acs.jpca.4c07364

Squaric Acid Core Substituted Unsymmetrical Squaraine Dyes for Dye-Sensitized Solar Cells: Effect of Electron Acceptors on Their Photovoltaic Performance

Safalmani Pradhan, Yuki Kurokawa, Suraya Shaban and Shyam S. Pandey

Colorants, 2023, 2, 654
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Engineering Exciton Dynamics with Synthetic DNA Scaffolds

Stephanie M. Hart, Jeffrey Gorman, Mark Bathe and Gabriela S. Schlau-Cohen

Acc. Chem. Res., 2023, 56, 2051
DOI: 10.1021/acs.accounts.3c00086

Ballistic Frenkel-exciton gate with a high on-off ratio

Aaron Sup, Bernard Yurke and Richard Elliott

Phys. Rev. A, 2024, 110
DOI: 10.1103/PhysRevA.110.022616