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Department of Materials Science and Engineering (MSE)
Yingling Research Group

Publications

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132. Akhlak U. Mahmood, Mehedi H. Rizvi, Joseph B. Tracy, Yaroslava G. Yingling, Molecular Insights into How Nanoparticle Agglomeration Inhibits Ligand Stripping, Advanced Materials Interfaces (2025),  DOI: 10.1002/admi.202500234

131. Cloud-based molecular dynamics simulations with AMBER: An interactive “collabortutorial” via Google Colab
Merve Fedai, Albert L. Kwansa, Yaroslava G. Yingling, (2025), Proceedings of the 2025 Biocatalyst Interactions with Gases (BIG) Research Symposium  https://ssrn.com/abstract=5282789

130. Advances in biomimetic carbonic anhydrase strategies for CO2 capture
Merve Fedai, Jialong Shen, Zsófia Bognár, Albert L. Kwansa, Amy Grunden, Stig Helveg, Sonja Salmon, and Yaroslava G. Yingling, Trends in Biotechnology (2025)  DOI:10.1016/j.tibtech.2025.05.025

129. DFT-based Calculation of Vibrational Sum Frequency Generation Spectrum of Non-Centrosymmetric Domains Interspersed in an Amorphous Matrix
Juseok Choi, Albert L. Kwansa, Inseok Chae, Yaroslava G. Yingling, and Seong H. Kim, J. Phys. Chem B (2025) DOI: 10.1021/acs.jpcb.5c00590

128. Jiangfeng Xu, Kirill Efimenko, Christopher B. Gorman, Yaroslava G. Yingling, Lisa Castellano, Jan Genzer, Functional hydrogels for selective phosphate removal from water and release on demand, Langmuir (2025), DOI: 10.1021/acs.langmuir.5c00679

127. Elizabeth Skelly, Christina J. Bayard, Joel Jarusek, Benjamin Clark, Laura Rebolledo, Yasmine Radwan, Phong Nguyen, Melanie Andrade-Muños, Thomas A. Deaton, Alexander Lushnikov, Sharonda J. LeBlanc, Alexey V. Krasnoslobodtsev, Yaroslava G. Yingling, Kirill A. Afonin, Design and Characterization of DNA-Driven Condensates: Regulating Topology, Mechanical Properties, and Immunorecognition, ACS Appl Mat Inter (2025) DOI: 10.1021/acsami.5c00428

126. Y. G. Yingling, M. M. Petrova, N. Yingling, The Role of AI in Water Quality Management, Water Conditioning and Purification, Water Conditioning & Purification International Magazine March (2025) 20-25, https://wcponline.com/2025/03/01/the-role-of-ai-in-water-quality-management/

125. Jaimie Marie Stewart, Yaroslava G. Yingling, Kirill A. Afonin, Florent Hubé, Naoyuki Kataoka, Editorial: Recent Advancements in RNA Technologies, Diagnostics, and Therapeutics, Frontiers in Bioengineering and Biotechnology 13 (2025), DOI: 10.3389/fbioe.2025.1550225

124. Nahed Abu Zaid, Kara Schatz, Kimberly Bourne, Darrell Harry, Christine Hendren, Anna-Maria Marshall, Khara Grieger, Jacob Jones, Alexey V. Gulyuk, Yaroslava G. Yingling, and Rada Chirkova, INTEGRATE-KG: A Workflow For Unifying Heterogeneous Data Driven by Shared Languages, 2024 IEEE International Conference on Big Data (BigData), Washington, DC, USA, (2024) 3522-3531, DOI:10.1109/BigData62323.2024.10825736.

123. Akhlak U. Mahmood, Minhazul Islam, Alexey V. Gulyuk, Emily Briese, Carmen A. Velasco, Mohit Malu, Naushita Sharma, Andreas Spanias, Yaroslava G. Yingling, and Paul Westerhoff, Multiple Data Imputation Methods Advances Risk Analysis and Treatability of Co-occurring Inorganic Chemicals in Groundwater, Environmental Science & Technology (2024), DOI:10.1021/acs.est.4c05203

122. Preeta Pratakshya, Albert L. Kwansa, Matic Kovačič, Nikhil Kaimal, Arsenii Panteleev, Atrouli Chatterjee, Nadia E. Tolouei, Rylan Kautz, Kyle L. Naughton, Barbara Sartori, Benedetta Marmiroli, MyAnh K. Dao, Sigrid Bernstorff, Janez Plavec, Yaroslava G. Yingling, Alon A. Gorodetsky, “Bulk Proton Conduction in Films from a Truncated Reflectin Variant”, APL Materials 12 (2024) 101113, DOI:10.1063/5.0214285

  • Chosen as an Editor’s Pick

121. Benjamin P. Allen, Sabila K. Pinky, Emily E. Beard, Abigail A. Gringeri, Nicholas Calzadilla, Matthew A. Sanders, Yaroslava G. Yingling, and Abigail S. Knight, Monomer Composition as a Mechanism to Control the Self-Assembly of Diblock Oligomeric Peptide–Polymer Amphiphiles, ACS Nano (2024), DOI:10.1021/acsnano.4c08028

120. Akhlak U. Mahmood, Melanie M. Ghelardini, Joseph B. Tracy, Yaroslava G. Yingling, Machine Learning and Small Data-Guided Optimization of Silica Shell Morphology on Gold Nanorods, Chemistry of Materials 36 (2024)  9330–9340, DOI:10.1021/acs.chemmater.3c03204

119. Faten B. Hussein, Andrew H. Cannon, Justin M. Hutchison, Christopher B. Gorman, Yaroslava G. Yingling, Brooke K. Mayer, “Phosphate-binding protein-loaded iron oxide particles: Adsorption performance for phosphorus removal and recovery from water”, Environmental Science: Water Research & Technology 10 (2024) 1219-1232 DOI:10.1039/D4EW00052H

118. Kara Schatz, Pei-Yu Hou, Alexey V. Gulyuk, Yaroslava G. Yingling, and Rada Chirkova, BUILD-KG: Integrating Heterogeneous Data Into Analytics-Enabling Knowledge Graphs, 2023 IEEE International Conference on Big Data (BigData), Sorrento, Italy, 2024 pp. 2965-2974, DOI: 10.1109/BigData59044.2023.10386570

117. Laine Taussig, Masoud Ghasemi, Sanggil Han, Albert L. Kwansa, Ruipeng Li, Nathan Woodward, Yaroslava G. Yingling, George G. Malliaras, Enrique D. Gomez, Aram Amassian, “Electrostatic Self-Assembly Induces Efficient Mixed Transport and Water Stability in PEDOT:PSS for High Performance OECTs”, Matter (2024), DOI: 10.2139/ssrn.4484649 

116. Albert L. Kwansa, Abhishek Singh, Justin T. Williams, Candace H. Haigler, Alison W. Roberts, Yaroslava G. Yingling, “Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods”, Cellulose 31 (2024) 1429-1447, DOI:10.1007/s10570-023-05691-x

115. Pei-Yu Hou, Jing Ao, Kara Schatz, Alexey V Gulyuk, Yaroslava G Yingling, Rada Chirkova, “Provenance-Aware Data Integration and Summarization Querying for Knowledge Graphs”, In: Delir Haghighi, P., et al. Information Integration and Web Intelligence. iiWAS 2023. Lecture Notes in Computer Science, vol 14416. Springer, Cham. (2023) DOI:0.1007/978-3-031-48316-5_29

  • Best Paper Award at the IIWAS: Information Integration and Web Intelligence Conference 2023, Bali, Indonesia

114. Juseok Choi, Albert L. Kwansa, Yaroslava G. Yingling, and Seong H. Kim, “DFT-Based Calculation of Molecular Hyperpolarizability and SFG Intensity of Symmetric and Asymmetric Stretch Modes of Alkyl Groups”, J. Phys. Chem B. 127 (2023) 8456-8467, DOI:10.1021/acs.jpcb.3c03910

113. Thomas J. Oweida, Yaroslava G. Yingling, “Resolving Structure of ssDNA in Solution by Fusing Molecular Simulations and Scattering Experiments with Machine Learning”, Advanced Theory and Simulations 6 (2023) 2300411, DOI:10.1002/adts.202300411

112. Christina J. Bayard and Yaroslava G. Yingling, “Computer-Assisted Design and peNJ) 2709 (2023) 31-49, DOI: 10.1007/978-1-0716-3417-2_2

111. Preeti Verma, Ruoya Ho, Albert L. Kwansa, Yaroslava G. Yingling, and Jochen Zimmer, “Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8”, Structure 31 (2023) 1-8, DOI: 10.1016/j.str.2023.07.010

110. Albert L. Kwansa, Rakhee C. Pani, Joseph A. DeLoach, Arianna Tieppo, Eric J. Moskala, Steven T. Perri, and Yaroslava G. Yingling, “Molecular mechanism of plasticizer exudation from polyvinyl chloride”, Macromolecules 56 (2023) 4775-4786, DOI: 10.1021/acs.macromol.2c01735

109. Akhlak U. Mahmood, Mehedi H. Rizvi, Joseph B. Tracy, Yaroslava G. Yingling, “Solvent Effects in Ligand Stripping Behavior of Colloidal Nanoparticles”, ACS Nano 17 (2023) 13319-13332, DOI: 10.1021/acsnano.3c01313

108. Buang Zhang, Sabila K. Pinky, Albert L. Kwansa, Spencer Ferguson, Yaroslava G. Yingling, Adrienne D. Stiff-Roberts, “Correlation of Emulsion Chemistry, Film Morphology, and Device Performance in Polyfluorene LEDs Deposited by RIR-MAPLE”, ACS Applied Materials & Interfaces 15 (2023) 18153-18165, DOI: 10.1021/acsami.3c03012

107. Sabila K. Pinky, Albert L. Kwansa, Buang Zhang, Adrienne D. Stiff-Roberts, Yaroslava G. Yingling, “Effect of Solvent on the Emulsion and Morphology of Polyfluorene Films: All-atom molecular dynamics approach”, Soft Matter 19 (2023) 1782-1790, DOI: 10.1039/D2SM01001A.

106. James S. Peerless, Alexey V. Gulyuk, Nina J. B. Milliken, Gyu Dong Kim, Elliot Reid, Jae Woo Lee, Dooil Kim, Zachary Hendren, Young Chul Choi, Yaroslava G. Yingling, “Role of Nanoscale Morphology on the Efficiency of Solvent-Based Desalination Method”, ACS EST Water 3 (2023) 400-409, DOI:10.1021/acsestwater.2c00473

105. Atrouli Chatterjeea, Preeta Pratakshyab, Albert L. Kwansa, Nikhil Kaimal, Andrew Cannon, Barbara Sartori, Benedetta Marmiroli, Helen Orins, Samantha Drake, Justin Couvrette, LeAnn Le, Sigrid Bernstorff, Yaroslava G. Yingling, Alon A. Gorodetsky, “Squid Skin Cell-Inspired Refractive Index Mapping of Cells, Vesicles, and Nanostructures”, ACS Biomaterials Science and Engineering 9 (2023) 978-990 DOI:10.1021/acsbiomaterials.2c00088

104. Jessica A. Nash, Matthew D. Manning, Alexey V. Gulyuk, Aleksey E. Kuznetsov, Yaroslava G. Yingling, “Gold Nanoparticle Design for dsRNA Compaction”, Biointerphases 17 (2022) 061001, DOI:10.1116/6.0002043

103. Juan Du, Venu Gopal Vandavasi, Kelly R. Molloy, Hui Yang, Lynnicia N. Massenburg, Abhishek Singh, Albert L. Kwansa, Yaroslava G. Yingling, Hugh O’Neill, Brian T. Chait, Manish Kumar, B. Tracy Nixon, “Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes”, Biomacromolecules 23 (2022) 3663-3677 DOI: 10.1021/acs.biomac.2c00550

102. Yuxin Xie, Nan K. Li, Abhishek Singh, Sanket A. Deshmukh, and Yaroslava G. Yingling, “A Comparison between the Lower Critical Solution Temperature Behavior of Polymers and Biomacromolecules”, PhysChem 2 (2022) 52-71; DOI:10.3390/physchem2010005

  • Invited Feature Paper
  • Most Highly Accessed Article
  • Highlighted on the front page

101. Akhlak U. Mahmood and Yaroslava G. Yingling, “All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles”, ACS Journal of Chemical Theory and Computations 18 (2022) 3122–3135, DOI: 10.1021/acs.jctc.1c01253

100. Benjamin P. Allen, Zoe M. Wright, Hailey F. Taylor, Thomas J. Oweida, Sabila Kader-Pinky, Emily F. Patteson, Kara M. Bucci, Caleb A. Cox, Abishec Sundar Senthilvel, Yaroslava G. Yingling, and Abigail S. Knight, “Mapping the Morphological Landscape of Oligomeric Di-block Peptide-Polymer Amphiphiles”, Angewandte Chemie 61 (2022) e202115547, DOI: 10.1002/anie.202115547

99. Morgan Chandler, Brian Minevich, Brandon Roark, Mathias Viard, M. Brittany Johnson, Mehedi H. Rizvi, Thomas A. Deaton, Seraphim Kozlov, Martin Panigaj, Joseph B. Tracy, Yaroslava G. Yingling, Oleg Gang, Kirill A. Afonin, “Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities”, ACS Applied Materials & Interfaces, 13 (2021) 39030-39041,  DOI: 10.1021/acsami.1c09230

98. Nan K. Li, Yuxin Xie and Yaroslava G. Yingling, “Insights into Structure and Aggregation Behavior of Elastin-like Polypeptide Coacervates: All-Atom Molecular Dynamics Simulations”, Journal of Physical Chemistry B 125 (2021) 8627-8635, DOI: 10.1021/acs.jpcb.1c02822

97. Jason N. Burris, Mohamadamin Makarem, Erin Slabaugh, Arielle Chaves, Ethan T. Pierce, Jongcheol Lee, Sarah N. Kiemle, Albert L. Kwansa, Abhishek Singh, Yaroslava G. Yingling, Alison W. Roberts, Seong H. Kim, and Candace H. Haigler, “Phenotypic effects of changes in the FTVTxK region of an Arabidopsis secondary wall cellulose synthase compared with results from analogous mutations in other isoforms”, Plant Direct 5 (2021) e355, DOI: 10.1002/pld3.335

  • Awarded Top Cited Article 2021-2022 by Wiley

96. James S. Peerless, Albert L. Kwansa, Branden S. Hawkins, Ralph C. Smith, Yaroslava G. Yingling, “Uncertainty Quantification and Sensitivity Analysis of Partial Charges on Macroscopic Solvent Properties in Molecular Dynamics Simulations with Machine Learning Model”, ACS Journal of Chemical Information and Modeling 61 (2021) 1745-1761 DOI: 10.1021/acs.jcim.0c01204

95. Hansol Lee, Aleksandr Stryutsky, Akhlak-Ul Mahmood, Abhishek Singh, Valery V. Shevchenko, Yaroslava G. Yingling, Vladimir V. Tsukruk, “Weakly Ionically Bound Thermo-sensitive Hyperbranched Polymers”, Langmuir 37 (2021) 2913-2927 DOI: 10.1021/acs.langmuir.0c03487

94. Thomas J. Oweida, Ho Shin Kim, Abhishek Singh, and Yaroslava G. Yingling, “Assessment of AMBER Force Fields for Simulations of ssDNA Structure”, ACS Journal of Chemical Theory and Computation 17 (2021) 1208-1217 DOI: 10.1021/acs.jctc.0c00931

93. Mehran J. Umerani, Preeta Pratakshya, Atrouli Chatterjee, Juana A. Cerna Sanchez, Ho Shin Kim, Gregor Ilc, Matic Kovačič, Christophe Magnan, Benedetta Marmiroli, Barbara Sartori, Albert L. Kwansa, Helen Orins, Andrew W. Bartlett, Erica M. Leung, Zhijing Feng, Kyle L. Naughton, Brenna Norton-Baker, Long Phan, James Long, Alex Allevato, Jessica E. Leal-Cruz, Qiyin Lin, Pierre Baldi, Sigrid Bernstorff, Janez Plavec, Yaroslava G. Yingling, Alon A. Gorodetsky, “Structure, Self-Assembly, and Properties of a Truncated Reflectin Variant”, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 32891-32901 DOI: 10.1073/pnas.2009044117

92. Rui Xiong, Abhishek Singh, Shengtao Yu, Shuaidi Zhang, Hansol Lee, Yaroslava G. Yingling, Dhriti Nepal, Timothy J. Bunning, Vladimir V. Tsukruk, “Co-assembling Polysaccharide Nanocrystals and Nanofibers for Robust Chiral Iridescent Films”, ACS Applied Materials & Interfaces 12 (2020) 35345–35353 DOI: 10.1021/acsami.0c08571

91. Nicholas G Taylor; Sang Hun Chung; Albert L Kwansa; Robert R Johnson III; Aaron J Teator; Nina J B Milliken; Karl M Koshlap; Yaroslava G Yingling; Yueh Z Lee; Frank Leibfarth, “Partially fluorinated copolymers as oxygen sensitive 19F MRI agents”, Chemistry – A European Journal 26 (2020) 9982-9990 DOI: 10.1002/chem.202001505

90. Abhishek Singh, Albert L. Kwansa, Ho Shin Kim, Justin T. Williams, Hui Yang, Nan K. Li, James D. Kubicki, Alison W. Roberts, Candace H. Haigler, Yaroslava G. Yingling, “In silico structure prediction of full-length cotton cellulose synthase protein (GhCESA1) and its hierarchical complexes”, Cellulose 27 (2020) 5597-5616 DOI: 10.1007/s10570-020-03194-7

89. Inseok Chae, Dien Ngo, Zhe Chen, Albert L. Kwansa, Xing Chen, Amira Barhoumi Meddeb, Nikolas J. Podraza, Yaroslava G. Yingling, Zoubeida Ounaies and Seong H. Kim, “Anisotropic optical and frictional properties of Langmuir–Blodgett film consisting of uniaxially-aligned rod-shaped cellulose nanocrystals”, Advanced Materials Interfaces 7 (2020) 1902169 DOI:10.1002/admi.201902169

88. Thomas J. Oweida, Akhlak Ul-Mahmood, Matthew D. Manning, Sergei Rigin, Yaroslava G. Yingling, “Merging Materials and Data Science: Opportunities, Challenges, and Education in Materials Informatics”, MRS Advances 5 (2020) 1-18 DOI: 10.1557/adv.2020.171

87. Ho Shin Kim, Nathanael A. Brown, Stefan Zauscher, and Yaroslava G. Yingling, “Effect of octadecylamine surfactant concentration on DNA structure on graphene surfaces”, Langmuir  36 (2020) 931-938 DOI:10.1021/acs.langmuir.9b02926

86. Jacob L. Jones, Yaroslava G. Yingling, Ian M. Reaney, and Paul Westerhoff, “Materials matter in phosphorus sustainability”, MRS Bulletin (2020), 45(1), 7-10 DOI:10.1557/mrs.2020.4

85. Felipe Garcia Quiroz, Nan K. Li, Stefan Roberts, Isaac Weitzhandler, Yaroslava G Yingling, Ashutosh Chilkoti, Intrinsically disordered proteins access a range of hysteretic phase separation behaviors, Science Advances 5 (2019) eaax5177 DOI: 10.1126/sciadv.aax5177

84. Chad Bradham, Abhishek Singh, Jozsef Stork, Ying Rong, Indrajit Kumar, Kazuhiro Kikuchi, Yaroslava G. Yingling, Tom P. Brutnell, Jocelyn K. C. Rose, Seth DeBolt, “Biochemical and physiological flexibility accompanies reduced cellulose biosynthesis in cesa1S830N”, AoB PLANTS 11 (2019) plz041 DOI: 10.1093/aobpla/plz041

83. Hui Yang, John McManus, Daniel Oehme, Abhishek Singh, Yaroslava G. Yingling, Ming Tien, James D. Kubicki, “Simulations of Cellulose Synthesis Initiation and Termination in Bacteria”, J Phys Chem B 123 (2019) 3699-3705 DOI: 10.1021/acs.jpcb.9b02433

•     Selected for journal cover page

82. Thomas A. Deaton, Fikret Aydin, Nan K. Li, Xiaolei Chu, Meenakshi Dutt and Yaroslava Yingling, “Dissipative Particle Dynamics Approaches to Modeling the Self-Assembly and Morphology of Neutral and Ionic Block Copolymers in Solution, Foundations of Molecular Modeling and Simulation”, Applications and Perspectives, Series Ed.: E. Maginn, book chapter (2021)  DOI: 10.1007/978-981-33-6639-8_4

81. Tom C. Gardinier, Ferdinand F. E. Kohle, James S. Peerless, Kai Ma, Melik Z. Turker, Joshua A. Hinckley, Yaroslava G. Yingling, and Ulrich Wiesner, “High Performance Chromatographic Characterization of Surface Chemical Heterogeneities of Fluorescent Organic-Inorganic Hybrid Core-Shell Silica Nanoparticles”, ACS Nano 13 (2) (2019) 1795–1804DOI: 10.1021/acsnano.8b07876

80. Matthew D. Manning, Albert L. Kwansa, Thomas Oweida, James Peerless, Abhishek Singh, Yaroslava G. Yingling, “Progress in ligand design for monolayer-protected nanoparticles for nano-bio interfaces”, Biointerphases 13 (2018) 06D502, DOI: 10.1116/1.5044381, invited review

  • Selected as a Featured Article;
  • News release Scilight, DOI:10.1063/1.5081027

79. James S. Peerless, Nina J. B. Milliken, Matthew D. Manning, Thomas J. Oweida, Yaroslava G. Yingling, “Soft Matter Informatics: Current Progress and Challenges”, Advanced Theory and Simulations 2 (2019) 1800129, DOI: 10.1002/adts.201800129, invited review

78. Michelle M. McGoorty, Abhishek Singh, Thomas A. Deaton, Benjamin Peterson, Chelsea M. Taliaferro, Yaroslava G. Yingling, and Felix N. Castellano, “Bathophenanthroline Disulfonate Ligand-induced Self-assembly of Ir(III) Complexes in Water: An Intriguing Class of Photoluminescent Soft Materials”, ACS Omega 3 (2018) 14027-14038 DOI: 10.1021/acsomega.8b02034

77. Renpeng Gu, Thomas Oweida, Yaroslava G. Yingling, Ashutosh Chilkoti, Stefan Zauscher, “Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation”, Biomacromolecules 19 (2018) 3525-3535 DOI: 10.1021/acs.biomac.8b00816

76. Nan K. Li, Stefan Roberts, Felipe Garcia Quiroz, Ashutosh Chilkoti, and Yaroslava G. Yingling, “Sequence directionality dramatically affects LCST behavior of elastin-like polypeptides”, Biomacromolecules 19 (2018) 2496-2505 DOI: 10.1021/acs.biomac.8b00099

75. Rui Xiong, Ho Shin Kim, Lijuan Zhang, Volodymyr F. Korolovych, Shuaidi Zhang, Yaroslava G. Yingling, and Vladimir V. Tsukruk, “Hairy Graphenes: Wrapping Nanocellulose Nets around Graphene Oxide Sheets”, Angewandte Chemie 130 (2018) 8644-8649 DOI:10.1002/anie.201803076

74. Tess R. Scavuzzo-Duggan, Arielle M. Chaves, Abhishek Singh, Latsavongsakda Sethaphong, Erin Slabaugh, Yaroslava G. Yingling, Candace H. Haigler, and Alison W. Roberts, “Cellulose synthase ‘class specific regions’ are intrinsically disordered and functionally undifferentiated”, Journal of Integrative Plant Biology 60 (2018) 481-497 DOI: 10.1111/jipb.12637

73. Ho Shin Kim, Thomas J. Oweida, and Yaroslava G. Yingling, “Interfacial Stability of Graphene-based Surfaces in Water and Organic Solvents”, Journal of Materials Science (invited Special Issue) 53(8) (2018), 5766-5776 DOI: 10.1007/s10853-017-1893-9

72. Linying Li, Nan K. Li, Qing Tu, Owen Im, Chia-Kuei Mo, Wei Han, William H. Fuss, Nick J. Carroll,  Ashutosh Chilkoti, Yaroslava G. Yingling, Stefan Zauscher and Gabriel P. López, “Functional Modification of Silica through Enhanced Adsorption of Elastin-Like Polypeptide Block Copolymers”, Biomacromolecules 19 (2018) 298-306 DOI: 10.1021/acs.biomac.7b01307

71. Rui Xiong, Ho Shin Kim, Shuaidi Zhang, Sunghan Kim, Volodymyr F. Korolovych, Ruilong Ma, Yaroslava G. Yingling, Canhui Lu, and Vladimir V. Tsukruk, “Template-Guided Assembly of Silk Fibroin on Cellulose Nanofibers for Robust Nanostructures with Ultrafast Water Transport”, ACS Nano 11 (2017) 12008-12019 DOI: 10.1021/acsnano.7b04235

70. Nan K. Li, Huihui Kuang, William H. Fuss, Stefan Zauscher, Efrosini Kokkoli, and Yaroslava G. Yingling, “Salt responsive morphologies of ssDNA-based triblock polyelectrolytes in semi-dilute regime: effect of volume fractions and polyelectrolyte length”, Macromolecular Rapid Communications 38 (2017) 700422 DOI: 10.1002/marc.201700422

•     Selected for journal cover page

69. James S. Peerless, G. Hunter Bowers, Albert L. Kwansa, and Yaroslava G. Yingling, “Effect of C60 Adducts on the Dynamic Structure of Aromatic Solvation Shells”, Chem. Phys. Letters 678(2017) 79-84 DOI: 10.1016/j.cplett.2017.04.010

68. Qing Tu, Ho Shin Kim, Thomas J. Oweida, Zehra Parlak, Yaroslava G. Yingling, Stefan Zauscher, “Interfacial Mechanical Properties of Graphene on Self Assembly Monolayers: Experiments and Simulations”, ACS Applied Materials and Interfaces 9(2017) 10203-10213 DOI: 10.1021/acsami.6b16593

67. Ho Shin Kim, Barry L. Farmer, and Yaroslava G. Yingling, “Effect of graphene oxidation rate on adsorption of poly-thymine single stranded DNA”, Advanced Materials Interfaces (2017) 1601168 DOI: 10.1002/admi.201601168

•     Selected for journal cover page

66. Jessica Nash, Albert Kwansa, James Peerless, Hoshin Kim, Yaroslava G. Yingling, “Advances in Molecular Modeling of Nanoparticle-Nucleic Acid Interfaces”, Bioconjugate Chemistry 28(2017) 3-10 DOI: 10.1021/acs.bioconjchem.6b00534

•     Selected for journal cover page

65. Brandon Roark, Anna Ivanina, Morgan Chandler, Jose Castaneda, Ho Shin Kim, Shriram Jawahar, Mathias Viard, Strahinja Talic, Kristin Wustholz, Yaroslava G. Yingling, Marcus Jones, Kirill A. Afonin, “Fluorescence blinking as an output signal for biosensing”, ACS Sensors 1 (2016) 1295–1300DOI: 10.1021/acssensors.6b00352

64. Jessica A. Nash, Tasha L. Tucker, William Therriault, and Yaroslava G. Yingling, “Binding of single stranded nucleic acids to ligand functionalized gold nanoparticles”, Biointerphases 11(2016) 04B305 DOI: 10.1116/1.4966653

63. Anise M. Grant, Ho Shin Kim, Trisha L. Dupnock, Kesong Hu, Yaroslava G. Yingling, Vladimir V. Tsukruk, “Silk Fibroin-Substrate Interactions at Heterogeneous Nanocomposite Interfaces”, Advanced Functional Materials 26 (2016) 6380-6392 DOI:10.1002/adfm.201601268

•     Selected for journal cover page

62. Wangyao Ge, Nan K. Li, Ryan D. McCormick, Eli Lichtenberg, Yaroslava G. Yingling and Adrienne D. Stiff-Roberts, “Emulsion-based RIR-MAPLE deposition of conjugated polymers: primary solvent effect and its implications on organic solar cell performance”, ACS Applied Materials and Interfaces 8 (2016) 19494-19506 DOI: 10.1021/acsami.6b05596

61.B. Tracy Nixon, Katayoun Mansouri, Abhishek Singh, Juan Du, Jonathan K. Davis, Jung-Goo Lee, Erin Slabaugh, Venu Gopal Vandavasi, Hugh O’Neill, Eric. M. Roberts, Alison W. Roberts, Yaroslava G. Yingling, Candace H. Haigler “Comparative structural and computational analysis supports eighteen cellulose synthases in the plant cellulose synthesis complex”, Scientific Reports 6 (2016) 28696 DOI:10.1038/srep28696

60.Ho Shin Kim, Doyoung Eom, Yoon-Mo Koo, and Yaroslava G. Yingling, “The effect of imidazolium cations on the structure and activity of the Candida antarctica Lipase B enzyme in ionic liquids”, Physical Chemistry Chemical Physics 18 (2016) 22062-22069 DOI: 10.1039/C6CP02355J

•     Selected for journal cover page

59. Ho Shin Kim, Sabrina M. Huang, Yaroslava G. Yingling, “Sequence dependent interaction of single stranded DNA with graphitic flakes: atomistic molecular dynamics simulations”, MRS Advances 1, 25 (2016) 1883-1889  DOI: 10.1557/adv.2016.91

58. Abhijit Rangnekar, Jessica A Nash, Bethany Goodfred, Yaroslava G. Yingling, and Thomas LaBean, “Design of potent and controllable anticoagulants using DNA aptamers and nanostructures”, Molecules 21 (2016) 202 DOI:10.3390/molecules21020202

57. Binwu Zhao, Nan K. Li, Yaroslava G. Yingling, and Carol K. Hall, “LCST Behavior is Manifested in a Single Molecule: Elastin-like polypeptide (VPGVG)n”, Biomacromolecules 17(2016) 111–118 DOI: 10.1021/acs.biomac.5b01235

56. Yagnesh Nagarajan, Jay Rongala, Sukanya Luang, Abhishek Singh, Nadim Shadiac, Julie Hayes, Tim Sutton, Matthew Gilliham, Stephen Tyerman, Gordon McPhee, Nicolas H. Voelcker, Hayden D. T. Mertens, Nigel Kirby, Jung-Goo Lee, Yaroslava G. Yingling, Maria Hrmova, “Na+-Dependent Anion Transport by a Barley Efflux Protein Revealed through an Integrative Platform”, Plant Cell 28 (2015) 202-218 DOI:10.1105/tpc.15.00625

55 Latsavongsakda Sethaphong, Jonathan K. Davis, Erin Slabaugh, Abhishek Singh, Candace H. Haigler, and Yaroslava G. Yingling, “Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis”, Cellulose 23 (2016) 145-161.DOI 10.1007/s10570-015-0789-6

•     Selected for journal cover page

54. James S. Peerless, G. Hunter Bowers, Albert L. Kwansa, and Yaroslava G. Yingling, “Fullerenes in Aromatic Solvents: Correlation between Solvation Shell Structure, Solvate Formation, and Solubility”, J. Phys. Chem. B 119 (2015) 15344-15352 DOI: 10.1021/acs.jpcb.5b09386

53. Jessica A. Nash, Abhishek Singh, Nan K. Li, and Yaroslava G. Yingling, “Characterization of nucleic acid compaction with histone-mimic nanoparticles through all-atom molecular dynamics”, ACS Nano 9 (2015) 12374-12382 DOI: 10.1021/acsnano.5b05684

52. Shundai Li, Lei Lei, Yaroslava G. Yingling, and Ying Gu, “Microtubules and cellulose biosynthesis: the emergence of new players”, Current Opinion in Plant Biology 28 (2015) 76-82, DOI: 10.1016/j.pbi.2015.09.002

51. Lei Lei, Abhishek Singh, Logan Bashline, Shundai Li, Yaroslava G. Yingling, and Ying Gu, “Cellulose synthase interactive 1 is required for a fast recycling of cellulose synthase complexes to the plasma membrane in Arabidopsis”, Plant Cell (2015),  DOI: 10.​1105/​tpc.​15.​00442

50. Nan K. Li, W. H. Fuss, L. Tang, R. Gu, A. Chilkoti, S. Zauscher, and Yaroslava G. Yingling, “Prediction of salt-dependent changes in morphology of polyelectrolyte block copolymers”, Soft Matter 11 (2015) 8236-8245, DOI: 10.1039/C5SM01742D

•     Selected for journal cover page

49. Hui Yang, J. Zimmer, Yaroslava G. Yingling, and J. D. Kubicki, “How cellulose elongates – A QM/MM study of the molecular mechanism of cellulose polymerization in bacteria CESA”, Journal of Physical Chemistry B 119(2015) 6525-6535. DOI: 10.1021/acs.jpcb.5b01433

48. Nan K. Li, W. H. Fuss, and Yaroslava G. Yingling, “An implicit ionic strength solvent (ISIS) method to model polyelectrolyte systems with dissipative particle dynamics”, Macromolecular Theory and Simulations 24 (2015) 7-12. DOI: 10.1002/mats.201400043  

•     Selected for journal cover page

47. Nan K. Li, F. García Quiroz, C. K. Hall, A. Chilkoti, and Yaroslava G. Yingling, “Molecular description of the LCST behavior of an elastin-like polypeptide”, Biomacromolecules 15 (2014) 3522–3530. DOI: 10.1021/bm500658w

46. Erin Slabaugh, L. Sethaphong, C. Xiao, J. Amick, C. T. Anderson, C. H. Haigler and Yaroslava G. Yingling, “Computational and genetic evidence that different structural conformations of a non-catalytic region in cellulose synthase (CESA) affect CESA function”, Journal of Experimental Botany 65 (2014) 6645-6653. DOI:10.1093/jxb/eru383

45. Nan K. Li, H. S. Kim, J. A. Nash, M. Lim, and Yaroslava G. Yingling, “Progress in molecular modeling of DNA materials”, Molecular Simulation 40 (2014)  777-783. DOI:10.1080/08927022.2014.913792

44. Lei Tang, V. Tjong, N. Li, Yaroslava G. Yingling, A. Chilkoti, and S. Zauscher, “Enzymatic polymerization of high molecular weight DNA amphiphiles that self-assemble into star-like micelles”, Advanced Materials 26 (2014) 3050-3054. DOI: 10.1002/adma.201306049

43. Ho S. Kim, S. H. Ha, L. Sethaphong, Y.-M. Koo, and Yaroslava G. Yingling, “The relationship between enhanced enzyme activity and structural dynamics in ionic liquids: a combined computational and experimental study”, Physical Chemistry Chemical Physics 16 (2014) 2944-2953. DOI: 10.1039/C3CP52516C

42. Erin Slabaugh, J. K. Davis, C. H. Haigler, Yaroslava G. Yingling, and J. Zimmer, “Cellulose synthases: new insights from crystallography and modeling”, Trends in Plant Science 19 (2013) 99-106. DOI:10.1016/j.tplants.2013.09.009

41. Rakhee C. Pani, B. D. Bond, G. Krishnan, and Yaroslava G. Yingling, “Correlating fullerenes diffusion with polythiophene morphology: molecular dynamics simulations”, Soft Matter 9 (2013) 10048-10055. DOI: 10.1039/C3SM51906F

40. Latsavongsakda Sethaphong, C. H. Haigler, J. D. Kubicki, J. Zimmer, D. Bonetta, S. DeBolt, and Yaroslava G. Yingling, “Tertiary model of a plant cellulose synthase”, Proceedings of the National Academy of Sciences of the USA (PNAS) 110 (2013) 7512-7517. DOI: 10.1073/pnas.1301027110

39. H. Yi, S. Thakur, L. Sethaphong, Yaroslava G. Yingling, “X3DBio2: A Visual Analysis Tool for Biomolecular Structure Exploration”, Proc. SPIE 8654 VDA (2013) 86540W. DOI: 10.1117/12.2002626

38. Ashley E. Marlowe, A. Singh, and Yaroslava G. Yingling, “The effect of point mutations on structure and mechanical properties of collagen-like fibril: a molecular dynamics study”, Materials Science and Engineering C 32 (2012) 2583-2588.DOI:10.1016/j.msec.2012.07.044

37. Rakhee Pani and Yaroslava G. Yingling, “Role of solvent and dendritic architecture on the redox core encapsulation”, Journal of Physical Chemistry A 116 (2012) 7593-7599. DOI:10.1021/jp304253g

36. Justin G. Railsback, A. Singh, R. C. Pearce, T. E. McKnight, R. Collazo, Z. Sitar, Yaroslava G. Yingling, and Anatoli V. Melechko, “Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation”, Advanced Materials 24 (2012) 4261-4265. DOI:10.1002/adma.201104891

35. H. Yi, A. Singh, and Yaroslava G. Yingling, “X3DBio: A Visual Analysis Tool for Biomolecular Structure Exploration”, Proc. SPIE 8294 (2012) 82940S-1-8. DOI:10.1117/12.906893

34. Ho S. Kim, R. Pani, S. H. Ha, Y.-M. Koo, and Yaroslava G. Yingling, The role of hydrogen bonding in water-mediated glucose solubility in ionic liquids, Journal of Molecular Liquids 166 (2012) 25-30. DOI:10.1016/j.molliq.2011.11.008

33. Melissa A. Pasquinelli and Yaroslava G. Yingling, “Perspective on nanoparticle-biomolecules interactions from molecular dynamics simulations” in Molecular Modeling and Its Role in Advancing Nanotechnology, Encyclopedia of Nanotechnology, B. Bhushan, Ed., v.3 (Springer, 2012) 1454-1463. ISBN 978-90-481-9750-7

•     Selected for journal cover page

32. Abhishek Singh, L. Sethaphong, and Yaroslava G. Yingling, “Interactions of cations with RNA loop-loop complexes”, Biophysical Journal 101 (2011) 727-735. DOI:10.1016/j.bpj.2011.06.033

•     Selected for journal cover page

31. Abhishek Singh, H. Eksiri, and Yaroslava G. Yingling, “Theoretical perspective on properties of DNA-functionalized surfaces”, Journal of Polymer Science B: Polymer Physics 49 (2011) 1563-1627. DOI:10.1002/polb.22349

•     Selected for journal cover page

30.   Abhishek Singh and Yaroslava G. Yingling, “Simulations of stretching single stranded DNA”, Mater. Res. Soc. Symp. Proc. 1303 (2011) mrsf10-1301-oo10-06.  DOI:10.1557/opl.2011.569

29. Abhishek Singh, S. Snyder, L. Lee, A. P. R. Johnston, F. Caruso, and Yaroslava G. Yingling, “Effect of Oligonucleotide Length on the Assembly of DNA Materials: Molecular Dynamics Simulations of Layer-by-Layer DNA Films”, Langmuir 26 (2010) 17339-17347. DOI:10.1021/la102762t

28. Latsavongsakda Sethaphong, A. Singh, A. E. Marlowe, and Yaroslava G. Yingling, “The sequence of HIV-1 TAR RNA helix controls cationic distribution”, Journal of Physical Chemistry C 114 (2010) 5506-5512. DOI:10.1021/jp906147q

27. Andrii V. Semichaevsky, A. E. Marlowe, and Yaroslava G. Yingling, “Comparing ion distributions around RNA and DNA helical and loop-loop motifs”, Mater. Res. Soc. Symp. Proc. 1130 (2009) W05-05. DOI: 10.1557/PROC1130W0505

26. Abhishek Singh and Yaroslava G. Yingling, “RNA molecular recognition and self-assembly into nanoparticles”, Proc. International Institute of Informatics and Systemics 1 (2009) 6-7. ISBN: 193427268X;978-193427268-8

25. Stacey Snyder and Yaroslava G. Yingling, “Computational Elucidation of the self-assembly of nucleic acids into novel materials”, Proc. International Institute of Informatics and Systemics 1 (2009) 8-9. ISBN: 193427268X;978-193427268-8

24. V. A. Stupina, A. Meskauskas, J. C. Mccormack, Yaroslava G. Yingling, B. A. Shapiro, J. D. Dinman, and A. E. Simon, “The 3′ Proximal Translational Enhancer of Turnip Crinkle Virus Binds to 60S Ribosomal Subunits”, RNA 14 (2008) 2379-2393. DOI:10.1261/rna.1227808

23. J. C. McCormack, X. Yuan, Yaroslava G. Yingling, W. Kasprzak, R. E. Zamora, B. A. Shapiro, and A. E. Simon, “Structural domains within the 3’ UTR of Turnip Crincle Virus”, Journal of Virology 82 (2008) 8706-8720 . DOI:10.1128/JVI.00416-08

  • B. A. Shapiro, E. Bindewald, W. Kasprzak, and Yaroslava G. Yingling, “Protocols for the In silico Design of RNA Nanostructures” in Nanostructure Design Methods and Protocols, Methods in Molecular Biology series, Vol. 474, E. Gazit and R. Nussinov, Eds., (Humana Press, 2008). ISBN 978-1-934115-35-0

21. E. Bindewald, R. Hayes, Yaroslava G. Yingling, W. Kasprzak, and B. A. Shapiro, “RNAJunction: A Database of RNA Junctions and Kissing Loops for Three-Dimensional Structural Analysis and Nanodesign”, Nucleic Acids Research 36 (2008) D392-D397. . DOI:10.1093/nar/gkm842

20. Yaroslava G. Yingling and B. A. Shapiro, “Computational design of an RNA hexagonal nano-ring and an RNA nanotube”, Nano Letters 7 (2007) 2328-2334. DOI:10.1021/nl070984r

19. B. A. Shapiro, Yaroslava G. Yingling, W. Kasprzak, and E. Bindewald, “Bridging the gap in RNA structure prediction”, Current Opinion in Structural Biology 17 (2007) 157-165. DOI: 10.1016/j.sbi.2007.03.001

18. M. Prasad, P. F. Conforti, B. J. Garrison, and Yaroslava G. Yingling, “Computational Investigation into the Mechanisms of UV Ablation of Poly (methyl methacrylate)”, Applied Surface Science 253 (2007) 6382-6385. DOI:10.1016/j.apsusc.2007.01.054

17. Yaroslava G. Yingling and B. J. Garrison, “Incorporation of chemical reactions into UV photochemical ablation of coarse-grained material”, Applied Surface Science 253 (2007) 6377-6381. DOI: 10.1016/j.apsusc.2007.01.100

16. Yaroslava G. Yingling and B. A. Shapiro, “The Impact of Dyskeratosis Congenita Mutations on Structure and Dynamics of the Telomerase RNA Pseudoknot Domain”, Journal of Biomolecular Structure and Dynamics 24 (2007), 303-320. DOI:10.1080/07391102.2007.10531238

•     Selected for journal cover page

15. Yaroslava G. Yingling and B. A. Shapiro, “The Prediction of the Wild-type Telomerase RNA Pseudoknot Structure and the Pivotal Role of a Bulge in its Formation”, Journal of Molecular Graphics and Modelling 25 (2006) 261-274. DOI: 10.1016/j.apsusc.2007.01.100

14. P. F. Conforti, Yaroslava G. Yingling, and B. J. Garrison, “Computational Studies of Ultraviolet Ablation of Poly(Methyl MethAcrylate)”, Journal of Physics: Conference Series 59 (2007), 322-327. DOI:10.1088/1742-6596/59/1/068

13. W. A. Hastings, Yaroslava G. Yingling, G. S. Chirikjian, and B. A. Shapiro, “Structural and Dynamical Classification of RNA Single-Base Bulges for Nanostructure Design”, Journal of Computational and Theoretical Nanoscience 3 (2006) 63-77. DOI:10.1166/jctn.2006.005

12. Yaroslava G. Yingling and B. A. Shapiro, “Dynamic Behavior of the Telomerase RNA Hairpin Structure and Its Relationship to Dyskeratosis Congenita”, Journal of Molecular Biology 348 (2005) 27-42. DOI: 10.1016/j.jmb.2005.02.015

11. Yaroslava G. Yingling and B. J. Garrison, “Coarse-Grained Model of Interaction of Light with Polymeric Material: Onset of Ablation”, Journal of Physical Chemistry B 109 (2005) 16482-16489. DOI: 10.1021/jp0527711

10. Yaroslava G. Yingling, P. F. Conforti, and B. J. Garrison, “Theoretical Investigation of Laser Pulse Width Dependence in Thermal Confinement Regime”, Applied Physics A 79 (2004) 757-759. DOI: 10.1007/s00339-004-2575-4

9.   Yaroslava G. Yingling and B. J. Garrison, “Coarse Grained Chemical Reaction Model”, Feature Article in J. Physical Chemistry B 108 (2004) 1815-1821. DOI: 10.1021/jp035730i

8.   Yaroslava G. Yingling, B. J. Garrison, “Photochemical Ablation of Organic Solids”, Nucl. Instrum. Methods Phys. Research B 203 (2003) 188-194. DOI:10.1016/S0168-583X(02)01855-4

7.   L. V. Zhigilei, Yaroslava G. Yingling, T. E. Itina, T. A. Schoolcraft, and B. J. Garrison, “MD Simulations of MALDesorption – Connections to Experiment”, Int. J. Mass Spectrom. 226 (2003) 85-106. DOI:10.1016/S1387-3806(02)00962-4

6.   L. V. Zhigilei, E. Leveugle, B. J. Garrison, Yaroslava G. Yingling, and M. I. Zeifman, “Computer Simulations of Laser Ablation of Molecular Substrates”, Chemical Reviews 103 (2003) 321-348. DOI: 10.1021/cr010459r

5.   J. Garrison, A. Delcorte, L. V. Zhigilei, T. E. Itina, K. D. Krantzman, Yaroslava G. Yingling, C. M. McQuaw, E. J. Smiley, and N. Winograd, “Big Molecule Ejection – SIMS vs. MALDI”, Applied Surface Science 69-71 (2003) 203-204. DOI : 10.1016/S0169-4332(02)00661-X

4.   Yaroslava G. Yingling and B. J. Garrison, “Photochemical induced effects in material ejection in laser ablation”, Chem. Phys. Letters 364 (2002) 237-243. DOI:10.1016/S0009-2614(02)01327-1

3.   Yaroslava G. Yingling, L. V. Zhigilei, and B. J. Garrison, “The Role of the Photochemical Fragmentation in Laser Ablation”, J. Photochemistry and Photobiology A: Chemistry 145 (2001) 173-181. DOI: 10.1016/S1010-6030(01)00580-9

2.   Yaroslava G. Yingling, L. V. Zhigilei, and B. J. Garrison, “Photochemical Fragmentation Processes in Laser Ablation of Organic Solids”, Nucl. Instrum. Methods Phys. Research B 180 (2001) 171-175. DOI: 10.1016/S0168-583X(01)00414-1

  1. Yaroslava G. Yingling, L. V. Zhigilei, B. J. Garrison, A. Koubenakis, J. Labrakis, and S. Georgiou, “Laser Ablation of Bi-component Systems: A Probe of Molecular Ejection Mechanisms”,  Applied Physics Letters 78 (2001) 1631-1633. DOI: 10.1063/1.1353816

Non-peer-reviewed publications

  1. Merve Fedai, Albert L. Kwansa, Yaroslava G. Yingling, Cloud-based molecular dynamics simulations with AMBER: An interactive “collabortutorial” via Google Colab (2025), Proceedings of the 2025 Biocatalyst Interactions with Gases (BIG) Research Symposium  https://ssrn.com/abstract=5282789
    1. GitHub link: https://github.com/yingling-group/BIG-MD/tree/v1
    1. Zenodo link: https://zenodo.org/records/15597021 
  2. T. E. Itina, O.Polit, A. Pastukhov, Y. Yingling, Z. Swiatkowska-Warkocka, A. Kabashin, Femtosecond Laser Fabrication of Plasmonic-Magnetic Ni-Au Nanoparticles with Enhanced Magnetic Properties, SPIE Proceedings Volume 13352, Nanoscale and Quantum Materials: From Synthesis and Laser Processing to Applications 2025; 1335209 (2025) DOI: 10.1117/12.3049889

Akshayaa Venkataraghavan, Ho Shin Kim, Julian G. Schwerdt, Alexey V. Gulyuk, Abhishek Singh, Yaroslava G. Yingling, Stephen D. Tyerman, Maria Hrmova, Barley HvNIP2;1 aquaporin permeates water, metalloids, saccharides, and ion pairs due to structural plasticity and diversification, bioRxiv (2023) 2023.04.17.537278  DOI:10.1101/2023.04.17.537278

Y. G. Yingling, M. M. Petrova, Natalia Yingling, The Role of AI in Water Quality Management, Water Conditioning and Purification, Water Conditioning & Purification International Magazine March (2025), https://wcponline.com/2025/03/01/the-role-of-ai-in-water-quality-management/