Journal Publications

2025

Shibani Basu, Simon K. Roy, Mandeep Sharma, German Barcenas, Bernard Yurke, William B. Knowlton, and Jeunghoon Lee, Site−specific Photo–crosslinking in a Double Crossover DNA tile Facilitated by Squaraine Dye Aggregates: Advancing Thermally Stable and Uniform DNA Nanostructures, Biomaterials Science, (2025). doi:10.1039/D4BM01695E.

2024

Nicholas D. Wright, Matthew S. Barclay, Sebastian A. Dıaz, Divita Mathur, Gregory A. Ellis, William B. Knowlton, Bernard Yurke, Paul H. Davis, Igor L. Medintz, Joseph S. Melinger, Ryan D. Pensack, and Daniel B. Turner, Varying Line-Broadening Sources by Tuning the Composition of DNA-Assembled Cyanine Tetramer Aggregates, The Journal of Physical Chemistry C, 128, 40, 17023–17037 (2024). doi: 10.1021/acs.jpcc.4c03246.
Gissela Pascual, Sebastián A. Díaz, Simon K. Roy, Adam Meares, Matthew Chiriboga, Kimihiro Susumu, Divita Mathur, Paul D. Cunningham, Igor L. Medintz, Bernard Yurke, William B. Knowlton, Joseph S. Melinger, Jeunghoon Lee, Towards tunable exciton delocalization in DNA Holliday junction-templated indodicarbocyanine 5 (Cy5) dye derivative heterodimers, Nanoscale Horizons, 9, 2334-2348 (2024). doi: 10.1039/D4NH00225C.
Maia Ketteridge, Devan Wat, Katelyn Duncan, German Barcenas, Kaden Shaw, William Knowlton, Bernard Yurke, Ryan Pensack, Olga Mass and Lan Li, Influence of substituents on the vectorial difference static dipole upon excitation in synthetic bacteriochlorins, The Journal of Physical Chemistry A, 128, 36, 7581–7592 (2024). doi:10.1021/acs.jpca.4c03821.
Jonathan S. Huff, Lance K. Patten, Daniel B. Turner, William B. Knowlton, Jeunghoon Lee, Bernard Yurke, and Ryan D. Pensack, Structural Insight into a Sixteen Cyanine Dye Construct via Exciton–Exciton Annihilation, The Journal of Physical Chemistry Letters, 15, 31, 8018–8025 (2024). doi: 10.1021/acs.jpclett.4c01622.
Aaron Sup, Bernard Yurke, and Richard Elliott, Ballistic Frenkel-exciton gate with a high on-off ratio, Physical Review A, 110, No. 2, 022616 (1-9), (2024). doi: 10.1103/PhysRevA.110.022616.

Alexander J. Rode, Paul C. Arpin, Daniel B. Turner, Theoretical model of femtosecond coherence spectroscopy of vibronic excitons in molecular aggregates, Journal of Chemical Physics, 160, 16, 164101 (1-16), (2024). doi:10.1063/5.0200570.
Keitel Cervantes-Salguero, Madison Kadrmas, Brett M. Ward, Drew Lysne, Amanda Wolf, Luca Piantanida, Gissela Pascual, William B. Knowlton, Minimizing Structural Heterogeneity in DNA Self-Assembled Dye Templating via DNA Origami-Tuned Conformations, Langmuir, 40, 19, 10195-10207, (2024). doi: 10.1021/acs.langmuir.4c00470.
Sebastián Díaz, Young Kim, Paul Cunningham, Divita Mathur, Igor Medintz, Donald Kellis, Bernard Yurke, William B. Knowlton, Joseph Melinger, Excitonically coupled cyanine dye dimers as energy transfer relays on DNA templates, ACS Applied Optical Materials, (2024). doi: 10.1021/acsaom.3c00459.
Matthew S. Barclay, Nicholas D. Wright, Paul Cavanaugh, Ryan D. Pensack, Eric W. Martin, and Daniel B. Turner, Ultrabroadband two-dimensional electronic spectroscopy in the pump-probe geometry using conventional optics, Optics Letters, 49, 8, 2065-2068, (2024). doi: doi.org/10.1364/OL.519387. Featured in Spotlight on Optics.
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, Effect of hydrophilicity-imparting substituents on exciton delocalization in squaraine dye aggregates covalently templated to DNA Holliday junctions, Nanoscale, 16, 1206-1222, (2024). (Featured in the special themed collection of Celebrating International Women’s day 2024: Women in Nanoscience presented by Nanoscale_RSC). doi: 10.1039/D3NR04499H.
William P. Carbery, Laurie A. Bizimana, Matthew S. Barclay, Nicholas C. Wright, Paul H. Davis, William B. Knowlton, Ryan D. Pensack, Paul C. Arpin, and Daniel B. Turner, Spatiotemporal Dispersion Compensation for a 200-THz Noncollinear Optical Parametric Amplifier, Review of Scientific Instruments, 95, 033002, (2024). doi: 10.1063/5.0187338.

2023

Shibani Basu, Simon Roy, German Barcenas, Lan Li, Bernard Yurke, William B. Knowlton, Jeunghoon Lee, Enhanced Photo−crosslinking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers, Biochemistry, 62 (22), 3234-3244 (2023).
Jonathan Huff, Katelyn Duncan, Cornelius J Van Galen, Matthew Barclay, William Knowlton, Bernard Yurke, Paul H Davis, Daniel B. Turner, Robert J. Stanley and Ryan D. Pensack, High-sensitivity electronic Stark spectrometer featuring a laser-driven light source, Review of Scientific Instruments, 94(9), 094103 (2023). doi: 10.1063/5.0153428.
Olga A. Mass, Devan Watt, Lance Patten, Jeunghoon Lee, Daniel Turner, Bernard Yurke, William B. Knowlton, Exciton Delocalization in Fully Synthetic DNA-Templated Bacteriochlorin Dimer, Physical Chemistry Chemical Physics, 25, 28437-28451, (2023). doi:10.1039/d3cp01634j.
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, Pursuing Excitonic Energy Transfer with Programmable DNA-based Optical Breadboards, Chemical Society Reviews, 52, 7848-794, (2023). doi:10.1039/d0cs00936a.
Bernard Yurke, “DNA assembly of dye aggregates—a possible path to quantum computing”, in “Visions of DNA nanotechnology at 40 for the next 40 – a tribute to Nadrian C. Seeman“, edited by N. Jonoska and E. Winfree (Springer, Singapore, 2023), pp. 125-169. doi:10.1007/978-981-19-9891-1_9.
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. Electronic Structure and Excited-State Dynamics of DNA-Templated Monomers and Aggregates of Asymmetric Polymethine Dyes, The Journal of Physical Chemistry A, 127(23), 4901-4918 (2023). doi: 10.1021/acs.jpca.3c00562.
Maia Ketteridge, Austin Biaggne*, Ryan Rau, German Barcenas*, Olga Mass, William Knowlton, Bernard Yurke and Lan Li. Effect of substituent location on the relationship between the transition dipole moments, difference static dipole, and hydrophobicity in squaraine dyes for quantum information devices, Molecules, 28(5), 2163 (2023). doi:10.3390/molecules28052163.
German Barcenas*, Austin Biaggne*, Olga A Mass, William B Knowlton, Bernard Yurke, and Lan Li. Molecular Dynamic Studies of Dye-Dye and Dye-DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions, International Journal of Molecular Science, 24(4), 4059 (2023). doi:10.3390/ijms24044059.
Sebastian A Diaz, Gissela Pascual, Lance K Patten, Adam Meares, Matthew Chiriboga, Kimihiro Susumu, Simon K Roy*, William B Knowlton, Paul D Cunningham, Divita Mathur, Bernard Yurke, Igor L Medintz, Jeunghoon Lee, and Joseph S Melinger, Towards Control of Excitonic Coupling in DNA-Templated Cy5 Aggregates: The Principal Role of Chemical Substituent Hydrophobicity and Steric Interactions, Nanoscale, 15, 3284-3299 (2023). doi:10.1039/D2NR05544A.
Matthew Barclay, Azhad Chowdhury, Austin Biaggne*, Jonathan Huff*, Nicholas Wright*, Paul Davis, Lan Li, Bill Knowlton, Bernard Yurke, Ryan Pensack, and Daniel Turner, Probing DNA Structural Heterogeneity by Identifying Conformational Subensembles of a Bicovalently Bound Cyanine Dye, The Journal of Chemical Physics, 158, 035101 (2023). doi: 10.1063/5.0131795.
Nicholas Wright*, Jonathan Huff*, Matthew Barclay, Christopher Wilson, German Barcenas*, Katelyn Duncan, Maia Ketteridge*, Olena Obukhova, Alexander Krivoshey, Anatoliy Tatarets, Ewald Terpetschnig, Jacob Dean, William Knowlton, Bernard Yurke, Lan Li, Olga Mass, Paul Davis, Jeunghoon Lee, Daniel Turner and Ryan Pensack, Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines, The Journal of Physical Chemistry A (Special issue on Physical Chemistry of Quantum Information Science), 127 (5), 1141–1157 (2023). doi:10.1021/acs.jpca.2c06442.
Bernard Yurke, Richard Elliott, and Aaron Sup, Implementation of a Frenkel Exciton-Based Controlled Phase Shifter, Physical Review A, 107, 012603 (2023). doi: 10.1103/PhysRevA.107.012603.

2022

Paul C. Arpin, Mihail Popa, and Daniel B. Turner, Signatures of Duschinsky Rotation in Femtosecond Coherence Spectra, AppliedMath, 2(4), 675‒686 (2022). doi.org/10.3390/appliedmath2040039.
Olga Mass, Shibani Basu, Lance Patten, Ewald Terpetschnig, Alexander Krivoshey, Anatoliy Tatarets, Ryan Pensack, Bernard Yurke, William Knowlton, and Jeunghoon Lee, Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction, Journal of Physical Chemistry Letters, 13, 10688−10696 (2022). doi: 10.1021/acs.jpclett.2c02721.
Katelyn M. Duncan, Donald L. Kellis, Jonathan S. Huff*, Matthew S. Barclay, Jeunghoon Lee, Daniel B. Turner, Paul H. Davis, Bernard Yurke, William B. Knowlton, and Ryan D. Pensack, Symmetry Breaking Charge Transfer in DNA-Templated Perylene Dimer, Molecules (Special Issue: Excitons in Molecular Aggregates), 27(19), 6612 (2022). doi: 10.3390/molecules27196612.
Paul Arpin and Daniel Turner, Perturbative Theoretical Model of Electronic Transient Circular Dichroism Spectroscopy of Molecular Aggregates, Journal of Chemical Physics, 157, 154101 (2022). doi: 10.1063/5.0119626.
Austin Biaggne*, Youngchan Kim, Joseph Melinger, William Knowlton, Bernard Yurke, and Lan Li, Molecular Dynamics Simulations of Cyanine Dimers Attached to DNA Holliday Junctions, RSC Advances, 12, 28063-28078 (2022). doi: 10.1039/d2ra05045e.
Jonathan Huff*, Sebastián Díaz, Matthew Barclay, Azhad Chowdhury, Matthew Chiriboga, Gregory Ellis, Divita Mathur, Lance Patten, Simon Roy*, Aaron Sup, Austin Biaggne*, Brian Rolczynski, Paul Cunningham, Lan Li, Jeunghoon Lee, Paul Davis, Bernard Yurke, William Knowlton, Igor Medintz, Daniel Turner, Joseph Melinger, and Ryan Pensack, Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes, Journal of Physical Chemistry C,126 (40), 17164‒17175 (2022). doi:10.1021/acs.jpcc.2c04336. doi: 10.1021/acs.jpcc.2c04336.
Keitel Cervantes-Salguero, Austin Biaggne*, John M. Youngsman, Brett M. Ward, Young C. Kim, Lan Li, John A. Hall, William B. Knowlton, Elton Graugnard, Wan Kuang, Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching, International Journal of Molecular Sciences, 23, 7690 (2022). doi:10.3390/ijms23147690.
Shibani Basu, Keitel Cervantes-Salguero, Bernard Yurke, William B. Knowlton, Jeunghoon Lee, Olga A. Mass, Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction, Molecules, 27, 13, 4006 (2022). doi:10.3390/molecules27134006.
Matthew S. Barclay, Jonathan S. Huff*, Ryan D. Pensack, Paul H. Davis, William B. Knowlton, Bernard Yurke, Jacob C. Dean, Paul C. Arpin, and Daniel B. Turner, Characterizing Mode Anharmonicity and Huang–Rhys Factors Using Models of Femtosecond Coherence Spectra, Journal of Physical Chemistry Letters 13, 24, 5413‒5423 (2022). doi:10.1021/acs.jpclett.1c04162.
Austin Biaggne*, Lawrence Spear, German Barcenas*, Maia Ketteridge*,Young C. Kim, Joseph S. Melinger, William B. Knowlton, Bernard Yurke, and Lan Li, Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates, Molecules 27, 11, 3456 (2022). doi: 10.3390/molecules27113456.
Barclay, MS, CK Wilson, SK Roy*, OA Mass, OM Obukhova, RP Svoiakov, AL Tatarets, AU Chowdhury, JS Huff*, DB Turner, PH Davis, EA Terpetschnig, B Yurke, WB Knowlton, J Lee, and RD Pensack, Oblique Packing and Tunable Excitonic Coupling in DNA-Templated Squaraine Rotaxane Dimer Aggregates, ChemPhotoChem, 6 (7), e202200039 (2022). Note: Top 10% of downloads for papers published in same Issue between 1st January 2022-31st December 2022. doi:10.1002/cptc.202200039.
Azhad Chowdhury, Sebastián Díaz , Jonathan Huff*, Matthew Barclay, Matthew Chiriboga, Gregory Ellis, Divita Mathur, Lance Patten, Aaron Sup, Natalya Hallstrom, Paul Cunningham, Jeunghoon Lee, Paul Davis, Daniel Turner, Bernard Yurke, William Knowlton, Igor Medintz, Joseph Melinger, and Ryan Pensack, Tuning Between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates, Journal of Physical Chemistry Letters 13, 12, 2782–2791 (2022). doi: 10.1021/acs.jpclett.2c00017.
Adam Meares, Kimihiro Susumu, Divita Mathur, Sang Ho Lee, Olga Mass, Jeunghoon Lee, Ryan Pensack, Bernard Yurke, William Knowlton, Joseph Melinger, and Igor Medintz, Synthesis of Substituted Cy5 Phosphoramidite Derivatives and Their Incorporation into Oligonucleotides Using Automated DNA Synthesis, ACS Omega 7, 13, 11002–11016 (2022). doi: 10.1021/acsomega.1c06921.
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, The Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates, Journal of Physical Chemistry C, 126, 7, 3475–3488 (2022). doi: 10.1021/acs.jpcc.1c08981.
Xiao Wang, Ruojie Sha, William B. Knowlton, Nadrian C. Seeman, James W. Canary, and Bernard Yurke, Exciton Delocalization in a DNA-Templated Organic Semiconductor Dimer Assembly, ACS Nano, 16, 1, 1301–1307 (2022). doi: 10.1021/acsnano.1c09143.

2021

Roy*, SK, OA Mass, DL Kellis, CK Wilson, JA Hall, B Yurke, and WB Knowlton, Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates, Journal of Physical Chemistry B, 125, 50, 13670–13684 (2021). doi: 10.1021/acs.jpcb.1c07602. Dataset doi:10.18122/quantum_data.1.boisestate.
Huff*, JS, DB Turner, OA Mass, LK Patten, CK Wilson, SK Roy*, MS Barclay, B Yurke, WB Knowlton, PH Davis, and RD Pensack, Excited-State Lifetimes of DNA-Templated Cyanine Dimer, Trimer, and Tetramer Aggregates: The Role of Exciton Delocalization, Dye Separation, and DNA Heterogeneity, J. Phys. Chem. B, 125(36): 10240–10259 (2021). doi: 10.1021/acs.jpcb.1c04517.
Barcenas*, G, A Biaggne*, OA Mass, CK Wilson, OM Obukhova, OS Kolosova, AL Tatarets, E Terpetschnig, RD Pensack, J Lee, WB Knowlton, B Yurke, and L Li, First-Principles Studies of Substituent Effects on Squaraine Dyes, RSC Advances, 11, 19029–19040 (2021). doi: 10.1039/d1ra01377g.
Jake T. Benzing, Olivia O. Maryon, Nik Hrabe, Paul H. Davis, Michael F. Hurley and Frank W. DelRio, Impact of grain orientation and phase on Volta potential differences in an additively manufactured titanium alloy, AIP Advances 11, 025219 (2021). doi: 10.1063/5.0038114.
Paul C. Arpin and Daniel B. Turner, Signatures of Vibrational and Electronic Quantum Beats in Femtosecond Coherence Spectra, Journal of Physical Chemistry A, 125(12), 2425–2435 (2021). doi: 10.1021/acs.jpca.0c10807.
Barclay, MS, SK Roy*, JS Huff*, OA Mass, DB Turner, CK Wilson, DL Kellis*, E Terpetschnig, J Lee, PH Davis, B Yurke, WB Knowlton, and RD Pensack, Rotaxane Rings Promote Oblique Packing and Extended Excited-State Lifetimes in DNA-Templated Squaraine Dye Aggregates, Communications Chemistry, 4 (19), 1–11 (2021). doi: 10.1038/s42004–021–00456–8. Selected to be included in the journal’s 2021 Editors’ Highlights collection.
Biaggne, A*, WB Knowlton, B Yurke, J Lee, and L Li, Substituent Effects on the Solubility and Electronic Properties of Cy5: Density Functional and Time-Dependent Density Functional Theory Calculations, Molecules, 26(3), 524 (2021). doi: 10.3390/molecules26030524.

2020

Drew Lysne, Kailee Jones, Alma Stosius, Tim Hachigian, Jeunghoon Lee, and Elton Graugnard, Availability-Driven Design of Hairpin Fuels and Small Interfering Strands for Leakage Reduction in Autocatalytic Networks, Journal of Physical Chemistry B, 124 (16), 3326–3335 (2020). doi: 10.1021/acs.jpcb.0c01229.
Olga A. Mass, Christopher K. Wilson, Simon K. Roy*, Lance K. Patten, Matthew S. Barclay, Ewald A. Terpetschnig, Jeunghoon Lee, Ryan D. Pensack, Bernard Yurke, and William B. Knowlton, Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds, Journal of Physical Chemistry B, 124 (43), 9636–9647 (2020). Cover page art. doi: 10.1021/acs.jpcb.0c06480.
Daniel B. Turner and Paul C. Arpin, Basis Set Truncation Further Clarifies Vibrational Coherence Spectra, Chemical Physics, 539, 110948 (2020). doi: 10.1016/j.chemphys.2020.110948.
Paul D. Cunningham, Sebastián A. Díaz, Bernard Yurke, Igor L. Medintz, and Joseph S. Melinger, Delocalized Two-Exciton States in DNA Scaffolded Cyanine Dimers, Journal of Physical Chemistry B, 124 (37), 8042–8049 (2020). doi: 10.1021/acs.jpcb.0c06732.

2019

Jonathan S. Huff*, Paul H. Davis, Allison Christy*, Donald L. Kellis*, Nirmala Kandadai, Zi S.D. Toa, Gregory D. Scholes, Bernard Yurke, William B. Knowlton, and Ryan D. Pensack, DNA-Templated Aggregates of Strongly-Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes, Journal of Physical Chemistry Letters, 10 (10), 2386–2392 (2019). doi: 10.1021/acs.jpclett.9b00404.
Donald L. Kellis*, Christopher Sarter*, Brittany L. Cannon*, Paul H. Davis, Elton Graugnard, Jeunghoon Lee, Ryan Pensack, Theresa Kolmar, Andres Jäschke, Bernard Yurke, and William B. Knowlton, An All-Optical Excitonic Switch Operated in the Liquid and Solid Phases, ACS Nano, 13 (3), 2986–2994 (2019). doi: 10.1021/acsnano.8b07504.
Friedrich C. Simmel, Bernard Yurke, and Hari R. Singh, Review – Principles and Applications of Nucleic Acid Strand Displacement Reactions, Chemical Reviews, 119 (10), 6326–6369 (2019). doi: 10.1021/acs.chemrev.8b00580.
C.M. Efaw*, T. da Silva*, P.H. Davis, L. Li, E. Graugnard, M.F. Hurley, Toward Improving Ambient Volta Potential Measurements with SKPFM for Corrosion Studies, Journal of the Electrochemical Society, 166 (11), C3018-C3027 (2019). This paper is part of the JES Focus Issue on Electrochemical Techniques in Corrosion Science in Memory of Hugh Isaacs. doi: 10.1149/2.0041911jes.
Muhammad Rizwan Rizwan Latif, Paul Davis, William Knowlton, Maria Mitkova, CBRAM Devices Based on a Nanotube Chalcogenide Glass Structure, Journal of Materials Science: Materials in Electronics, 30 (3), 2389–2402 (2019). doi: 0.1007/s10854-018-0512-0.

2018

Jenny Wren Fothergill*, Andres Correa Hernandez**, William B. Knowlton, Bernard Yurke, Lan Li, Ab-Initio Studies of Exciton Interaction, Journal of Physical Chemistry A, 122 (46), 8989–8997 (2018). doi:10.1021/acs.jpca.8b05237.
S. Takabayashi*, S. Kotani*, J. Flores-Estrada*, E. Spears*, J.E. Padilla, L.C. Godwin, E. Graugnard, W. Kuang, S. Sills, W.L. Hughes, Boron-Implanted Silicon Substrates for Physical Adsorption of DNA Origami, International Journal of Molecular Sciences, 19 (9), 2513 (2018). doi: 10.3390/ijms19092513.
Paul H. Davis, Chad S. Watson, Corey M. Efaw*, Lance Patten*, Courtney Hollar*, William B. Knowlton, and Peter Müllner, Localized Deformation in Ni-Mn-Ga Single Crystals, Journal of Applied Physics, 123 (21), 215102 (2018). Cover and featured article for this issue. doi: 10.1063/1.5026572.
Brittany L. Cannon*, Lance K. Patten*, Donald L. Kellis**, Paul H. Davis, Jeunghoon Lee, Elton Graugnard, Bernard Yurke, William B. Knowlton, Large Davydov Splitting and Strong Fluorescence Suppression: An Investigation of Exciton Delocalization and in DNA-Templated Holliday Junction Dye Aggregates, Journal of Physical Chemistry A, 122 (8), 2086-2095 (2018). doi: 10.1021/acs.jpca.7b12668.

2017

R.M. Zadegan, E.G. Lindau*, W.P. Klein*, C. Green*, E. Graugnard, B. Yurke, W. Kuang, W.L. Hughes, Twisting of DNA Origami from Intercalators, Scientific Reports 7 7382 (2017). doi: 10.1038/s41598-017-07796-3.
Brittany L. Cannon*, Donald L. Kellis**, Lance K. Patten*, Paul H. Davis, Jeunghoon Lee, Elton Graugnard, Bernard Yurke, William B. Knowlton, Coherent Exciton Delocalization in a Two-State DNA Templated Dye Aggregate System, Journal of Physical Chemistry A, 121 (37), 6905-6916 (2017). doi: 10.1021/acs.jpca.7b04344.
P.H. Davis, K. Robles**, K. Livingson**, S. Johns**, V.A. Ravi, E. Graugnard, and M.F. Hurley, Phase Separation in Ti-6Al-4V Alloys with Boron Additions for Biomedical Applications: Scanning Kelvin Probe Force Microscopy Investigation of Microgalvanic Couples and Corrosion Initiation, JOM, 69 1446 (2017). doi: 10.1007/s11837-017-2378-7.
C.M. Green*, K. Schutt**, N. Morris**, R.M. Zadegan, W.L. Hughes, W. Kuang, E. Graugnard, Metrology of DNA arrays by super-resolution microscopy, Nanoscale 9, 10205-10211 (2017). doi: 10.1039/C7NR00928C.
X. Olson*, S. Kotani*, B. Yurke, E. Graugnard, W.L. Hughes, Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids, Journal of Physical Chemistry B 121, 2594–2602 (2017). doi: 10.1021/acs.jpcb.7b01198.
X. Olson*, S. Kotani*, J.E. Padilla, S. Goltry*, N. Hallstrom, B. Yurke, W.L. Hughes, E. Graugnard, Availability: A Metric for Nucleic Acid Strand Displacement Systems, ACS Synthetic Biology 6, 84-93 (2017). doi: 10.1021/acssynbio.5b00231.

2016

E. Krueger, J. Shim, A. Fathizadeh, A.N. Chang*, B. Subei*, K.M. Yocham**, P.H. Davis, E. Graugnard, F. Khalili-Araghi, R. Bashir, D. Estrada, D. Fologea, Modelling and Analysis of Intercalant Effects on Circular DNA Conformation, ACS Nano 10 8910-8917 (2016). doi: 10.1021/acsnano.6b04876.
V. A. Chernenko, I. R. Aseguinolaza, V. Golub, O. Y. Salyuk, B. Muntifering, W. B. Knowlton, P. Müllner, and J.M. Barandiarána, Self-patterning of epitaxial Ni-Mn-Ga/MgO (001) thin films, Acta Materialia, 111 (2016) 194-201. doi: 10.1016/j.actamat.2016.03.065.
Benjamin Reinholz, Steffen Brinckmann, Alexander Hartmaier, Brittany Muntifering, William B. Knowlton, Peter Mullner, Influence of the Twin Microstructure on the Mechanical Properties in Magnetic Shape Memory Alloys, Acta Materialia, 108, (2016) 197-206. doi: 10.1016/j.actamat.2016.02.007.
B. Muntifering, L. Kovarik, N. D. Browning, R. C. Pond, W. B. Knowlton, P. Müllner, Stress-assisted removal of conjugation boundaries in non-modulated Ni-Mn-Ga by coordinated secondary twinning, Journal of Materials Science (50th anniversary special Issue), 51 (1), (2016) 457-466. doi: 10.1007/s10853-015-9236-1.

2015

Rizal F. Hariadi, Erik Winfree, and Bernard Yurke, Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics, Proceedings of the National Academy of Science, 112 (45), (2015) E6086-E6095. doi:10.1073/pnas.1424673112.
Donald L. Kellis**, Sara Rehn**, Brittany Cannon*, Paul H. Davis, Elton Graugnard, Jeunghoon Lee, Bernard Yurke, William B. Knowlton, DNA-Mediated Excitonic Upconversion FRET Switching, New Journal of Physics, 17 (2015) 115007. doi: 10.1088/1367-2630/17/11/115007.
Sara Goltry*, Natalya Hallstrom, Tyler Clark**, Wan Kuang, Jeunghoon Lee, Cheryl Jorcyk, William B. Knowlton, Bernard Yurke, William L. Hughes, Elton Graugnard, DNA topology influences molecular machine lifetime in human serum, Nanoscale 7, 10382-10390 (2015). doi: 10.1039/C5NR02283E.
Brittany L. Cannon*, Donald L. Kellis**, Paul H. Davis, Jeunghoon Lee, Wan Kuang, William L. Hughes, Elton Graugnard, Bernard Yurke, William B. Knowlton, Excitonic AND Logic Gates on DNA Brick Nanobreadboards, ACS Photonics 2, 398-404 (2015). doi: 10.1021/ph500444d.
J. S. Hyslop**, A. R. Boydstun, T. R. Fereday, J. R. Rusch, J. L. Strunk, C. T. Wall, C. C. Pena, N. L. McKibben, J. D. Harris, A. Thurber*, A. Punnoose, J. Brotherton, P. Walker**, L. Lowe**, B. Rapp**, S. Purnell**, W. B. Knowlton, S. M. Hubbard and B. J. Frost, Synthesis and characterization of [Zn(acetate)2(amine)x] compounds (x=1 or 2) and their use as precursors to ZnO , Materials Science in Semiconductor Processing 38, 278-289 (2015). doi: 10.1016/j.mssp.2015.04.001.
Hurley, M. F., Efaw, C. M., Davis, P. H., Croteau, J. R., Graugnard, E. & Birbilis, N. Volta Potentials Measured by Scanning Kelvin Probe Force Microscopy as Relevant to Corrosion of Magnesium Alloys Corrosion 71, 160-170 (2015). doi: 10.5006/1432.

2014

Sadao Takabayashi*, William P. Klein*, Craig Onodera, Blake Rapp*, Elias Lindau*, Lejmarc Snowball**, Juan Flores-Estrada**, Joseph Tyler Sam**, Jeunghoon Lee, William B. Knowlton, Elton Graugnard, Bernard Yurke, Wan Kuang, and William L. Hughes, High Precision, High Yield Fabrication of Nanoparticle Arrays via DNA Origami Nanotube Directed Self-Assembly, Nanoscale, 6, 13928–13938 (2014). doi: 10.1039/C4NR03069A.

2013

Robert Schreiber, Ngoc Luong**, Zhiyuan Fan, Anton Kuzyk, Philipp C. Nickels, Tao Zhang, David M. Smith, Bernard Yurke, Wan Kuang, Alexander O. Govorov, and Tim Liedl, Chiral Plasmonic DNA Nanostructures with Switchable Circular Dichroism, Nature Communications 4, 2948 (2013). doi: 10.1038/ncomms3948.
William P. Klein*, Charles N. Schmidt**, Blake Rapp*, Sadao Takabayashi*, William B. Knowlton, Jeunghoon Lee, Bernard Yurke, William L. Hughes, Elton Graugnard, and Wan Kuang, Multi-Scaffold DNA Origami Nanoparticle Waveguides, Nano Letters 13 (8), 3850–3856 (2013). doi: 10.1021/nl401717y.
Herbert M. Huttanus*, Elton Graugnard, Bernard Yurke, William B. Knowlton, Wan Kuang, William L. Hughes, and Jeunghoon Lee, Enhanced DNA Sensing via Catalytic Aggregation of Gold Nanoparticles, Biosensors and Bioelectronics, 50, 382–386 (2013). doi: 10.1016/j.bios.2013.06.063.
C.S. Watson, C. Hollar**, K. Anderson**, W.B. Knowlton, P. Müllner, Magnetomechanical Four-State Memory, Advanced Functional Materials, 23 (32), 3995-4001 (2013). doi: 10.1002/adfm.201203015.

2012

Previtera, M. L., Chippada, U., Schloss, R. S., Yurke, B., Langrana, N. A., “Mechanical properties of DNA-crosslinked polyacrylamide hydrogels with increasing crosslinker density,” BioResearch Open Access 1, 256-259 (2012). doi: 10.1089/biores.2012.9906.
Schulman, R., Yurke, B., Winfree, E., “Robust self-replication of combinatorial information via crystal growth and scission,” Proceedings of the National Academy of Sciences (US) 109, 6405-6410 (2012). doi: 10.1073/pnas.1117813109.
I.R. Aseguinolaza, I. Reyes-Salazar, A.V. Svalov, K. Wilson*, W.B. Knowlton, P. Müllner, J.M. Barandiarán, E. Villa and V.A. Chernenko, Transformation volume strain in Ni-Mn-Ga thin films, Applied Physics Letters, 101, 241912 (2012). doi: 10.1063/1.4772005.
Ngoc Luong**, Cheng-Wen Cheng*, Min-Hsiung Shih, and Wan Kuang, Phase matching for surface plasmon enhanced second harmonic generation in a gold grating slab, Appl. Phys. Lett. 100, 181107 (2012). doi: 10.1063/1.4710546.
Elton Graugnard, Donald L. Kellis**, Hieu Bui, Stephanie Barnes*, Wan Kuang, Jeunghoon Lee, William L. Hughes, William B. Knowlton, and Bernard Yurke, DNA-controlled excitonic switches, Nano Letters 12(4), 2217 (2012). doi: 10.1021/nl3004336.
Harish Chandran, Nikhil Gopalkrishnan, Bernard Yurke and John Reif, Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions, Journal of the Royal Society Interface, published online 11 January 2012, doi: 10.1098/rsif.2011.0819.

2011

L. Vandelli, A. Padovani, L. Larcher, R.G. Southwick III*, W.B. Knowlton, and G. Bersuker, A Physical Model of the Temperature Dependence of the Current Through the SiO₂/High-K Stacks, IEEE Transactions On Electron Devices, 58 (9), (2011) 2878-2887. doi: 10.1109/TED.2011.2158825.

Alex English*, Cheng-Wen Cheng, Lloyd Lowe II**, Min-Hsiung Shih, Wan Kuang, Hydrodynamic Modeling of Surface Plasmon Enhanced Photon Induced Current in a Gold Grating, Applied Physics Letters, 191113 (2011). doi:10.1063/1.3590200.
Southwick III*, R.G., A. Sup, A. Jain, and W.B. Knowlton, An Interactive Simulation Tool For Complex Multilayer Dielectric Devices, IEEE Transactions on Device and Materials Reliability, 11 (2), 236 – 243 (2011). (Note: In IEEE TDMR Top 20 List of Accessed Articles for January 2012). doi: 10.1109/TDMR.2011.2129593.

2010

Bernard Yurke and Wan Kuang, Passive Linear Nanoscale Optical and Molecular Electronics Device Synthesis from Nanoparticles, Physical Review A 81, 033814 (2010). doi: 10.1103/PhysRevA.81.033814.
Hieu Bui*, Craig Onodera*, Carson Kidwell**, YerPeng Tan*, Elton Graugnard, Wan Kuang, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, and William L. Hughes, Programmable Periodicity of Quantum Dot Arrays with DNA Origami Nanotubes, Nano Letters 10, p. 3367-3372 (2010). doi: 10.1021/nl101079u.
Elton Graugnard, Amber Cox**, Jeunghoon Lee, Cheryl Jorcyk, Bernard Yurke, and William L. Hughes, Kinetics of DNA and RNA Hybridization in Serum and Serum-SDS, IEEE Transactions on Nanotechnology 9(5), p. 603-609 (2010). doi: 10.1109/TNANO.2010.2053380.
Wan Kuang, Alex English*, Zi-Chang Chang, Min-Hsiung Shih, William B Knowlton, Jeunghoon Lee, William Hughes, Bernard Yurke, Cavity Resonant Mode in a Metal film Perforated with Two-Dimensional Triangular Lattice Hole Arrays, Optics Communications 283(20), p. 4090-4093 (2010). doi: 10.1016/j.optcom.2010.05.055
Matthew Reinhold*, Chad Watson, William B. Knowlton, Peter Müllner, Transformation twinning of Ni-Mn-Ga characterized with temperature-controlled atomic force microscopy, Journal of Applied Physics – 107, 113501 (2010). doi: 10.1063/1.3429090.
Southwick* III, Richard G., Justin C. Reed**, Christopher Buu*, Ross Butler**, Gennadi Bersuker, and William B. Knowlton, Limitations of Poole-Frenkel Conduction in Bilayer HfO2/SiO2 MOS Devices, IEEE Transactions on Device and Materials Reliability, 10(2), pp. 201-207 (2010). (Note: In IEEE TDMR Top 10 List of Accessed Articles for September 2010). doi: 10.1109/TDMR.2009.2039215.

2009

M. Reinhold**, D. Kiener, W.B. Knowlton, G. Dehm, and P. Müllner, Deformation twinning in Ni-Mn-Ga micropillars with 10M martensite, Journal of Applied Physics (accepted for publication without revisions) 106, pp. 053906 (1-6) (2009). doi: 10.1063/1.3211327.
Sorcha Yingst*, Kaci Bloxham**, Lisa Warner*, Raquel Brown, Jennifer Cole*, Linda Kenoyer, William B. Knowlton, Julia Thom Oxford, Characterization of Collagenous Matrix Assembly in a Chondrocyte Model System, Journal of Biomedical Materials Research Part A, 90A (1), pp. 247-255 (2009). doi: 10.1002/jbm.a.32078.

2008

P.M. Lenahan, B Knowlton, J.F. Conley, B. Tonti, J. Suehle, and T. Grasser, Introduction to the Special Issue on the 2007 International Reliability Workshop, IEEE Transactions on Device and Materials Reliability, 8(3), (2008) p. 490. doi: 10.1109/TDMR.2008.2006011.
D. Estrada**, M. L. Ogas*, R. G. Southwick III*, P. M. Price**, R. J. Baker, W. B. Knowlton, Impact of Single pMOSFET Dielectric Degradation on NAND Circuit Performance, Microelectronics Reliability, 48(3), p. 354-363 (2008). doi: 10.1016/j.microrel.2007.09.002.
J. Jozwiak, R. G. Southwick III*, V. N. Johnson*, W. B. Knowlton, and A. J. Moll, Integrating through-wafer interconnects with active devices and circuits, IEEE Transactions on Advanced Packaging, special issue on wafer level packaging, Digital Object Identifier: 10.1109/TADVP.2007.906235, 31(1), p. 4-13 (2008). doi: 10.1109/TADVP.2007.906235.
P. Müllner, Z. Clark**, L. Kenoyer, W. B. Knowlton, and G. Kostorz, Nanomechanics of orthorhombic Ni-Mn-Ga martensite, Materials Science and Engineering A, Digital Object Identifier:10.1016/j.msea.2006.12.215, 481-482, p. 66-72 (2008). doi: 10.1016/j.msea.2006.12.215.

2007

K. M. Reddy, R. Benson*, Z. Clark**, R. Hansen*, J. Hays*, A. Thurber*, M. H. Engelhard, V. Shutthanandan, S. Thevuthasan, W. B. Knowlton and A. Punnoose, On the Room Temperature Ferromagnetism of Zn1-xCrxO Thin films Deposited by Reactive Co-sputtering, Solar Energy Materials & Solar Cells, 91, pp. 1496-1502 (2007). doi: 10.1016/j.solmat.2007.03.012.

2006

John F. Conley, Jr., Yuan Chen, Bill Knowlton, Tim Sullivan, Bill Tonti, Guest Editorial: Introduction to the Special Issue on the 2005 International Reliability Workshop, IEEE Transactions on Device and Materials Reliability, 6(2), (2006) p. 115-116. doi: 10.1109/TDMR.2006.877374.
R.G. Southwick III* and W.B. Knowlton, Stacked Dual Oxide MOS Energy Band Diagram Visual Representation Program, IRW student paper, Invited Paper, IEEE Transactions on Device and Materials Reliability, 6 (2), 136 – 145 (2006). doi: 10.1109/TDMR.2006.876971.

2002

John F. Conley, Jr., Yuan Chen, Bill Knowlton, Tim Sullivan, Bill Tonti, Guest Editorial: Introduction to the Special Issue on the 2005 International Reliability Workshop, IEEE Transactions on Device and Materials Reliability, 6(2), (2006) p. 115-116. doi: 10.1109/TDMR.2006.877374.

2001

Amy J. Moll, William B. Knowlton, David E. Bunnell, and Susan L. Burkett, Materials Science and Engineering at Boise State University: Responding to an Industrial Need, The Journal of Materials Education, 23, 83-88 (2001).

1998

Schnee, R.W., Akerib,-D.-S.; Barnes,-P.-D.-,-Jr.; Bauer,-D.-A.; Brink,-P.-L.; Cabrera,-B.; Caldwell,-D.-O.; Clarke,-R.-M.; Colling,-P.; Crisler,-M.-B.; DaSilva,-A.; Davies,-A.-K.; Dougherty,-B.-L.; Eichblatt,-S.; Irwin,-K.-D.; Gaitskell,-R.-J.; Golwala,-S.-R.; Haller,-E.-E.; Jochum,-J.; Knowlton,-W.-B.; Kuzminov,-V.; Nam,-S.-W.; Novikov,-V.; Penn,-M.-J.; Perera,-T.-A.; Ross,-R.-R.; Sadoulet,-B.; Shutt,-T.; Smith,-A.; Sonnenschein,-A.-H.; Spadafora,-A.-L.; Stockwell,-W.-K.; Yellin,-S.; Young,-B.-A., Results and status of the Cryogenic Dark Matter Search (CDMS), Physics-Reports, 307(1-4), 283-90 (Dec. 1998). doi: 10.1016/S0370-1573(98)00071-4.

1996

Shutt, T., D.S. Akerib, P.D. Barnes, Jr., A. Cummings, A. Da Silva, R. Diaz, J. Emes, S.R. Golwala, E.E. Haller, K. Itoh, B. Knowlton, F. Quéinnec, R.R. Ross, B. Sadoulet, D. Seitz, G. Smith, W. Stockwell, T. Trumbull, R. Therrien, S. White, and B.A. Young, Recent results with a 62 g Ge cryogenic dark matter detector, Nuclear Instruments & Methods in Physics Research A, 370, 165 (1996). doi: 10.1016/0168-9002(95)01367-9.
Sadoulet, B., D. Akerib, P. Barnes, Jr., A. Cummings, A.D. Silva, R. Diaz, J. Emes, S. Golwala, E.E. Haller, K. Itoh, W. Knowlton, F. Queinnec, R.R. Ross, D. Seitz, T. Shutt, G. Smith, W. Stockwell, and S. White, Particle detection and non-equilibrium phonons: experience with large germanium crystals and NTD Ge thermistors, Physica B, 219-220, 741-743 (1996). doi: 10.1016/0921-4526(95)00871-3.
Barnes, P.D., Jr., D.S. Akerib, D. Bauer, P. Brink, B. Cabrera, D.O. Caldwell, B. Chugg, R.M. Clarke, A. Cummings, A. Davies, R. Diaz, B.L. Dougherty, J. Emes, S.R. Golwala, D. Hale, E.E. Haller, K.D. Irwin, W.B. Knowlton, V. Kuziminov, A. Lu, S.W. Nam, M.J. Penn, V. Novikov, B.V. Pritychenko, F. Quéinnec, R.R. Ross, B. Sadoulet, D. Seitz, T. Shutt, A. Smith, G. Smith, A. Sonnenschein, W. Stockwell, J.D. Taylor, R. Therrien, T. Trumbull, S. White, R.C. Wolgast, S. Yellin, and B.A. Young, Installation of the cryogenic dark matter search (CDMS), Nuclear Instruments & Methods in Physics Research A, 370, 233 (1996). doi: 10.1016/0168-9002(95)01094-7.

1993

Knowlton, W.B., K.M. Itoh, J.W. Beeman, J.H. Emes, D. Loretto, and E.E. Haller, Ge-Au eutectic bonding of Ge {100} Crystals, Journal of Low Temperature Physics, 93, 343-348 (1993). doi: 10.1007/BF00693444.