Publications

112. Computer-Assisted Design and Characterization of RNA Nanostructures

Christina J. Bayard and Yaroslava G. Yingling Methods in Molecular Biology (Clifton, NJ)  2709 (2023) 31-49 DOI: 10.1007/978-1-0716-3417-2_2

111. Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8

Preeti Verma, Ruoya Ho, Albert L. Kwansa, Yaroslava G. Yingling, and Jochen Zimmer Structure  31 (2023) 1-8 DOI: 10.1016/j.str.2023.07.010

110. Molecular Mechanism of Plasticizer Exudation from Polyvinyl Chloride

Albert L. Kwansa, Rakhee C. Pani, Joseph A. DeLoach, Arianna Tieppo, Eric J. Moskala, Steven T. Perri, and Yaroslava G. Yingling Macromolecules  56 (2023) 4775-4786 DOI:10.1021/acs.macromol.2c01735

109. Solvent Effects in Ligand Stripping Behavior of Colloidal Nanoparticles

Akhlak U. Mahmood, Mehedi H. Rizvi, Joseph B. Tracy, Yaroslava G. Yingling ACS Nano  (2023) DOI:10.1021/acsnano.3c01313 Selected for Journal Cover

108. Correlation of Emulsion Chemistry, Film Morphology, and Device Performance in Polyfluorene LEDs Deposited by RIR-MAPLE

Buang Zhang, Sabila K. Pinky, Albert L. Kwansa, Spencer Ferguson, Yaroslava G. Yingling, Adrienne D. Stiff-Roberts ACS Applied Materials & Interfaces  15 (2023) 18153-18165 DOI:10.1021/acsami.3c03012

107. Effect of Solvent on the Emulsion and Morphology of Polyfluorene Films: All-atom molecular dynamics approach

Sabila K. Pinky, Albert L. Kwansa, Buang Zhang, Adrienne D. Stiff-Roberts, Yaroslava G. Yingling Soft Matter  19 (2023) 1782-1790 DOI: 10.1039/D2SM01001A

106. Role of Nanoscale Morphology on the Efficiency of Solvent-Based Desalination Method

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 ACS EST Water  3 (2023) 400-409 DOI:10.1021/acsestwater.2c00473

105. Squid Skin Cell-Inspired Refractive Index Mapping of Cells, Vesicles, and Nanostructures

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 ACS Biomaterials Science and Engineering 9 (2023) 978-990  DOI:10.1021/acsbiomaterials.2c00088 Selected for Journal Cover

104. Gold Nanoparticle Design for dsRNA Compaction

Jessica A. Nash, Matthew D. Manning, Alexey V. Gulyuk, Aleksey E. Kuznetsov, Yaroslava G. Yingling Biointerphases 17 (2022) 061001 DOI:10.1116/6.0002043 Selected as a Featured Article News release Scilight, DOI:10.1063/10.0014998

103. Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes

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 Biomacromolecules 23 (2022) 3663-3677DOI: 10.1021/acs.biomac.2c00550

102. A Comparison between the Lower Critical Solution Temperature Behavior of Polymers and Biomacromolecules

Yuxin Xie, Nan K. Li, Abhishek Singh, Sanket A. Deshmukh, and Yaroslava G. Yingling PhysChem 2 (2022) 52-71 DOI:10.3390/physchem2010005 Featured on the front page

101. All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles

Akhlak U. Mahmood and Yaroslava G. Yingling ACS Journal of Chemical Theory and Computations (2022) DOI: 10.1021/acs.jctc.1c01253 News release Journal Cover

100. Mapping the Morphological Landscape of Oligomeric Di-block Peptide-Polymer Amphiphiles

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,Abigail S. Knight Angewandte Chemie (2022) DOI: 10.1002/anie.202115547

99. Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities

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 ACS Applied Materials & Interfaces 13 (2021) 39030-39041 DOI: 10.1021/acsami.1c09230

98. Insights into Elastin-like Polypeptides Coacervates Structure and Aggregation Behavior: All-atom Molecular Dynamics Simulations

Nan K. Li, Yuxin Xie and Yaroslava G. Yingling Journal of Physical Chemistry B 125 (2021) 8627-8635 DOI:10.1021/acs.jpcb.1c02822

97. Phenotypic effects of changes in the FTVTxK region of an Arabidopsis secondary wall cellulose synthase compared with results from analogous mutations in other isoforms

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 Plant Direct 5 (2021) e335 DOI: 10.1002/pld3.335

96. Uncertainty Quantification of Atomistic Partial Charges for the Prediction of Solvent Properties via Molecular Dynamics Simulations

James S. Peerless, Albert L. Kwansa, Branden S. Hawkins, Ralph C. Smith, Yaroslava G. Yingling ACS Journal of Chemical Information and Modeling 61 (2021) 1745-1761 DOI: 10.1021/acs.jcim.0c01204 Journal Cover

95. Weakly Ionically Bound Thermo-sensitive Hyperbranched Polymers

Hansol Lee, Aleksandr Stryutsky, Akhlak-Ul Mahmood, Abhishek Singh, Valery V. Shevchenko, Yaroslava G. Yingling, Vladimir V. Tsukruk Langmuir 37 (2021) 2913-2927 DOI: 10.1021/acs.langmuir.0c03487

94. Assessment of AMBER Force Fields for Simulations of ssDNA Structure

Thomas J. Oweida, Ho Shin Kim, Abhishek Singh, and Yaroslava G. Yingling ACS Journal of Chemical Theory and Computation 17 (2021) 1208-1217 DOI: 10.1021/acs.jctc.0c00931

93. Structure, self-assembly, and properties of a truncated reflectin variant

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, and Alon A. Gorodetsky Proceedings of the National Academy of Sciences of the United States of America  117 (2020) 32891-32901 DOI: 10.1073/pnas.2009044117

92. Co-assembling Polysaccharide Nanocrystals and Nanofibers for Robust Chiral Iridescent Films

Rui Xiong, Abhishek Singh, Shengtao Yu, Shuaidi Zhang, Hansol Lee, Yaroslava G. Yingling, Dhriti Nepal, Timothy J. Bunning, Vladimir V. Tsukruk ACS Applied Materials & Interfaces 12 (2020) 35345-35353 DOI: 10.1021/acsami.0c08571

91. Partially fluorinated copolymers as oxygen sensitive 19F MRI agents

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 Chemistry – A European Journal 26 (2020) 9982-9990 DOI: 10.1002/chem.202001505

90. In silico structure prediction of full-length cotton cellulose synthase protein (GhCESA1) and its hierarchical complexes

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 Cellulose 27 (2020) 5597-5616 DOI: 10.1007/s10570-020-03194-7

89. Anisotropic optical and frictional properties of Langmuir–Blodgett film consisting of uniaxially-aligned rod-shaped cellulose nanocrystals

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 Advanced Materials Interfaces 7 (2020) 1-18 DOI:10.1002/admi.201902169

88. Merging Materials and Data Science: Opportunities, Challenges, and Education in Materials Informatics

Thomas J. Oweida, Akhlak Ul-Mahmood, Matthew D. Manning, Sergei Rigin, Yaroslava G. Yingling MRS Advances 5 (2020) 1-18 DOI: 10.1557/adv.2020.171

87. Effect of octadecylamine surfactant concentration on DNA structure on graphene surfaces

Ho Shin Kim, Nathanael A. Brown, Stefan Zauscher, and Yaroslava G. Yingling Langmuir 36 (2020) 931-938  DOI:10.1021/acs.langmuir.9b02926

86. Materials matter in phosphorus sustainability

Jacob L. Jones, Yaroslava G. Yingling, Ian M. Reaney, and Paul Westerhoff MRS Bulletin 5 (2020) 45(1), 7-10 DOI:10.1557/mrs.2020.4

85. Intrinsically disordered proteins access a range of hysteretic phase separation behaviors

Felipe Garcia Quiroz, Nan K. Li, Stefan Roberts, Patrick Weber, Michael Dzuricky, Isaac Weitzhandler, Yaroslava G. Yingling and Ashutosh Chilkoti Science Advances 5 (2019) eaax5177 DOI: 10.1126/sciadv.aax5177

84. Biochemical and physiological flexibility accompanies reduced cellulose biosynthesis in Brachypodium cesa1 S830N

Chad Brabham, Abhishek Singh, Jozsef Stork, Ying Rong, Indrajit Kumar, Kazuhiro Kikuchi, Yaroslava G Yingling, Thomas P Brutnell, Jocelyn K C Rose, Seth DeBolt AoB PLANTS 11 (2019) plz041 DOI:10.1093/aobpla/plz041

83. Simulations of Cellulose Synthesis Initiation and Termination in Bacteria

Hui Yang, John B. McManus, Daniel Oehme, Abhishek Singh, Yaroslava G Yingling, Ming Tien, and James D. Kubicki J. Phys. Chem. B 123 (2019) 3699-3705 DOI:10.1021/acs.jpcb.9b02433 Cover

82. Dissipative Particle Dynamics Approaches to Modeling the Self-Assembly and Morphology of Neutral and Ionic Block Copolymers in Solution

Thomas A. Deaton, Fikret Aydin, Nan K. Li, Xiaolei Chu, Meenakshi Dutt and Yaroslava Yingling Molecular Modeling and Simulation, Applications and Perspectives, Series Ed.: E. Maginn (2019) book chapter

81. High-Performance Chromatographic Characterization of Surface Chemical Heterogeneities of Fluorescent Organic–Inorganic Hybrid Core–Shell Silica Nanoparticles

Thomas C. Gardinier, Ferdinand F. E. Kohle, James S. Peerless, Kai Ma, Melik Z. Turker, Joshua A. Hinckley, Yaroslava G. Yingling, and Ulrich Wiesner ACS Nano 13 (2019) 1795-1804 DOI: 10.1021/acsnano.8b07876

80. Progress in ligand design for monolayer-protected nanoparticles for nano-bio interfaces

Matthew D. Manning, Albert L. Kwansa, Thomas Oweida, James Peerless, Abhishek Singh, Yaroslava G. Yingling Biointerphases 13 (2018) 06D502 DOI: 10.1116/1.5044381 Selected as a Featured Article; Scilight

79. Soft Matter Informatics: Current Progress and Challenges

James S. Peerless, Nina J. B. Milliken, Matthew D. Manning, Thomas J. Oweida, Yaroslava G. Yingling Advanced Theory and Simulations(2018) DOI: 10.1002/adts.201800129 Scraping tool https://github.com/yingling-group/flory_fox_scraper Top downloaded paper 2018-2019 by Wiley, Advanced Theory and Simulations

78. Bathophenanthroline Disulfonate Ligand-induced Self-assembly of Ir(III) Complexes in Water: An Intriguing Class of Photoluminescent Soft Materials

Michelle M. McGoorty, Abhishek Singh, Thomas A. Deaton, Benjamin Peterson, Chelsea M. Taliaferro, Yaroslava G. Yingling, and Felix N. Castellano ACS Omega (2018) 14027-14038 DOI: 10.1021/acsomega.8b02034

77. Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation

Renpeng Gu, Thomas Oweida, Yaroslava G. Yingling, Ashutosh Chilkoti, Stefan Zauscher Biomacromolecules (2018) DOI: 10.1021/acs.biomac.8b00816

76. Sequence directionality dramatically affects LCST behavior of elastin-like polypeptides

Nan K. Li, Stefan Roberts, Felipe Garcia Quiroz, Ashutosh Chilkoti, and Yaroslava G. Yingling Biomacromolecules (2018) DOI: 10.1021/acs.biomac.8b00099

75. Wrapping Nanocellulose Nets around Graphene Oxide Sheets

Rui Xiong, Ho Shin Kim, Lijuan Zhang, Volodymyr F. Korolovych, Shuaidi Zhang, Yaroslava G. Yingling, and Vladimir V. Tsukruk Angewandte Chemie International Edition 57 (2018) 8508-8513 DOI:10.1002/anie.201803076

74. Cellulose synthase ‘class specific regions’ are intrinsically disordered and functionally undifferentiated

Tess R. Scavuzzo-Duggan, Arielle M. Chaves, Abhishek Singh, Latsavongsakda Sethaphong, Erin Slabaugh, Yaroslava G. Yingling, Candace H. Haigler, and Alison W. Roberts Journal of Integrative Plant Biology 53 (2018) 5766-5776 DOI:10.1002/anie.201803076

73. Interfacial Stability of Graphene-based Surfaces in water and organic solvents

Ho Shin Kim, Thomas J. Oweida, and Yaroslava G. Yingling Journal of Materials Science (Invited Special Issue) 53 (2018) 5766–5776 DOI: 10.1007/s10853-017-1893-9 Selected as Springer April finalist for the 2018 Cahn Prize

72. Functional Modification of Silica through Enhanced Adsorption of Elastin-Like Polypeptide Block Copolymers

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 Biomacromolecules (2018) DOI: 10.1021/acs.biomac.7b01307

71. Template-Guided Assembly of Silk Fibroin on Cellulose Nanofibers for Robust Nanostructures with Ultrafast Water Transport

Rui Xiong, Ho Shin Kim, Shuaidi Zhang, Sunghan Kim, Volodymyr F. Korolovych, Ruilong Ma, Yaroslava G. Yingling, Canhui Lu, and Vladimir V. Tsukruk ACS Nano (2017) DOI: 10.1021/acsnano.7b04235

70. Salt responsive morphologies of ssDNA-based triblock polyelectrolytes in semi-dilute regime: effect of volume fractions and polyelectrolyte length

Nan K. Li, Huihui Kuang, William H. Fuss, Stefan Zauscher, Efrosini Kokkoli and Yaroslava G. Yingling Macromolecular Rapid Communications 38 (2017) 1700422 DOI: 10.1002/marc.201700422 Cover

69. Effect of C60 Adducts on the Dynamic Structure of Aromatic Solvation Shells

James S. Peerless, G. Hunter Bowers, Albert L. Kwansa, Yaroslava G. Yingling Chemical Physics Letters 678 (2017) 79-84 DOI: 10.1016/j.cplett.2017.04.010

68. Interfacial Mechanical Properties of Graphene on Self-Assembled Monolayers: Experiments and Simulations

Qing Tu, Ho Shin Kim, Thomas J. Oweida, Zehra Parlak, Yaroslava G Yingling, and Stefan Zauscher ACS Applied Materials and Interfaces 9 (2017) 10203-10213 DOI: 10.1021/acsami.6b16593

67. Effect of graphene oxidation rate on adsorption of poly-thymine single stranded DNA

Hoshin Kim, Barry L. Farmer, and Yaroslava G. Yingling Advanced Materials Interfaces (2017) DOI: 10.1002/admi.201601168 Cover

66. Advances in Molecular Modeling of Nanoparticle-Nucleic Acid Interfaces

Jessica A. Nash, Albert L. Kwansa, James S. Peerless, Hoshin Kim, Yaroslava G. Yingling Bioconjugate Chemistry 28 (2017) 3-10 DOI: 10.1021/acs.bioconjchem.6b00534 Cover

65. Fluorescence blinking as an output signal for biosensing

Brandon Roark, Jenna A. Tan, Anna Ivanina, Morgan Chandler, Jose Castaneda, Ho Shin Kim, Shriram Jawahar, Mathias Viard, Strahinja Talic, Kristin L. Wustholz, Yaroslava G Yingling, Marcus Jones, and Kirill A Afonin ACS Sensors 1 (2016) 1295-1300 DOI: 10.1021/acssensors.6b00352

64. Binding of single stranded nucleic acids to cationic ligand functionalized gold nanoparticles

Jessica A. Nash, Tasha L. Tucker, William Therriault, Yaroslava G. Yingling Biointerphases 11 (2016) 04B305 DOI: 10.1116/1.4966653

63. Silk Fibroin-Substrate Interactions at Heterogeneous Nanocomposite Interfaces

Anise M. Grant, Ho Shin Kim, Trisha L. Dupnock, Kesong Hu, Yaroslava G. Yingling, Vladimir V. Tsukruk Advanced Functional Materials 26 (2016) 6380-6392 DOI: 10.1002/adfm.201601268 Cover

62. Emulsion-based RIR-MAPLE deposition of conjugated polymers: primary solvent effect and its implications on organic solar cell performance

Wangyao Ge, Nan K. Li, Ryan D. McCormick, Eli Lichtenberg, Yaroslava G. Yingling and Adrienne D. Stiff-Roberts ACS Applied Materials and Interfaces 8 (2016) 19494-19506 DOI: 10.1021/acsami.6b05596

61. Comparative structural and computational analysis supports eighteen cellulose synthases in the plant cellulose synthesis complex

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 Scientific Reports 6 (2016) 28696 DOI:10.1038/srep28696

60. Role of Imidazolium Cation on Structure and Activity of Candida antarctica Lipase B Enzyme in Ionic Liquids

Ho Shin Kim, Doyoung Eom, Yoon-Mo Koo, and Yaroslava G. Yingling Physical Chemistry Chemical Physics 18 (2016) 22062-22069 DOI: 10.1039/C6CP02355J Cover

59. Sequence dependent interaction of single stranded DNA with graphitic flakes: atomistic molecular dynamics simulations

Ho Shin Kim, Sabrina M. Huang, Yaroslava G. Yingling MRS Advances 1(2016) 1883-1889 DOI: 10.1557/adv.2016.91

58. Design of potent and controllable anticoagulants using DNA aptamers and nanostructures

Abhijit Rangnekar, Jessica A Nash, Bethany Goodfred, Yaroslava G. Yingling, and Thomas LaBean Molecules 21 (2016) 202 DOI: 10.3390/molecules21020202

57. LCST Behavior is Manifested in a Single Molecule: Elastin-like polypeptide (VPGVG)n

Binwu Zhao, Nan K. Li, Yaroslava G. Yingling, and Carol K. Hall Biomacromolecules 17 (2016) 111-118 DOI: 10.1021/acs.biomac.5b01235

56. Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis

Latsavongsakda Sethaphong, Jonathan K. Davis, Erin Slabaugh, Abhishek Singh, Candace H. Haigler, Yaroslava G. Yingling Cellulose 23 (2016) 145-161 DOI: 10.1007/s10570-015-0789-6 Cover

55. Na+ Dependent Anion Transport by a Barley Efflux Protein Revealed through an Integrative Platform

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 Plant Cell 28 (2016) 202-218 DOI: 10.1105/tpc.15.00625 In Brief by K. L. Farquharson “Integrative Study Reveals Sodium Dependence of a Barley Borate Transporter” Reported on Phys.Org

54. Fullerenes in Aromatic Solvents: Correlation between Solvation Shell Structure, Solvate Formation, and Solubility

James S. Peerless, G. Hunter Bowers, Albert L. Kwansa, and Yaroslava G. Yingling J. Phys. Chem. B 119 (2015) 15344–15352 DOI: 10.1021/acs.jpcb.5b09386

53. Characterization of nucleic acid compaction with histone-mimic nanoparticles through all-atom molecular dynamics

Jessica A. Nash, Abhishek Singh, Nan K. Li, and Yaroslava G. Yingling ACS Nano 9 (2015) 12374-12382 DOI: 10.1021/acsnano.5b05684 Reported on Science 360

52. Microtubules and cellulose biosynthesis: the emergence of new players

Shundai Li, Lei Lei, Yaroslava G. Yingling, and Ying Gu Current Opinion in Plant Biology 28 (2015) 76-82 DOI: 10.1016/j.pbi.2015.09.002

51. Cellulose synthase interactive 1 is required for a fast recycling of cellulose synthase complexes to the plasma membrane in Arabidopsis

Lei Lei, Abhishek Singh, Logan Bashline, Shundai Li, Yaroslava G. Yingling, and Ying Gu Plant Cell (2015) DOI: 10.1105/tpc.15.00442

50. Prediction of solvent-induced morphological changes of polyelectrolyte diblock copolymer micelles

Nan K. Li, William H. Fuss, L. Tang, R. Gu, A. Chilkoti, S. Zauscher, Yaroslava G. Yingling Soft Matter 11 (2015) 8236-8245 DOI: 10.1039/C5SM01742D Cover Image

49. How Cellulose Elongates – a QM/MM Study of the Molecular Mechanism of Cellulose Polymerization in Bacterial CESA
H. Yang, J. Zimmer, Y.G. Yingling, J. D. Kubicki
Journal of Physical Chemistry B 119 (2015) 6525-6535

48. An Implicit Solvent Ionic Strength (ISIS) Method to Model Polyelectrolyte Systems with Dissipative Particle Dynamics
N. K. Li, W. H. Fuss, Y. G. Yingling
Macromolecular Theory and Simulations 24 (2015) 7-12.

• • • Reported in Materials today, Science Daily
    • Cover Image
    • Video

47. Molecular description of the LCST behavior of an elastin-like poly-peptide
N. K. Li, F. García Quiroz, C. K. Hall, A. Chilkoti, Y. G. Yingling
Biomacromolecules 15 (2014) 3522-3530

46. Computational and genetic evidence that different structural conformations of a non-catalytic region affect the function of plant cellulose synthase
E. Slabaugh, L. Sethaphong, C. Xiao, J. Amick, C. T. Anderson, C. H. Haigler, Y. G. Yingling
Journal of Experimental Botany 65 (2014) 6645-6653.

45. Progress in molecular modeling of DNA materials
N. K. Li, H. S. Kim, J. A. Nash, M. Lim, Y. G. Yingling
Molecular Simulation 40 (2014) 777-783.

44. Enzymatic polymerization of high molecular weight DNA amphiphiles that self-assemble into star-like micelles
L. Tang, V. Tjong, N. Li, Y. G. Yingling, A. Chilkoti, S. Zauscher
Advanced Materials 26 (2014) 3050-3054.

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

42. Cellulose synthases: new insights from crystallography and modeling
E. Slabaugh, J. K. Davis, C. H. Haigler, Y. G. Yingling, J. Zimmer
Trends in Plant Science 19 (2013) 99-106.

41. Correlating fullerenes diffusion with polythiophene morphology: molecular dynamics simulations
R. C. Pani, B. D. Bond, G. Krishnan, Y. G. Yingling
Soft Matter 9 (2013) 10048-10055

40. Tertiary model of a plant cellulose synthase
L. Sethaphong, C. H. Haigler, J. D. Kubicki, J. Zimmer, D. Bonetta, S. DeBolt, Y. G. Yingling
Proc. Natl. Acad. Sci. USA 110 (2013) 7512-7517

• • • Selected for F1000 Prime

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

• • • Download X3DBio2 software

38. The effect of point mutations on structure and mechanical properties of collagen-like fibril: a molecular dynamics study
A. E. Marlowe, A. Singh, Y. G. Yingling
Materials Science and Engineering C 32 (2012) 2583-2588

37. Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation
J. G. Railsback, A. Singh, R. C. Pearce, T. E. McKnight, R. Collazo, Z. Sitar, Y. G. Yingling, A. Melechko
Advanced Materials 24 (2012) 4261-4265

• • • Reported in Materials360, nanowiki
    • Cover Image

36. Role of Solvent and Dendritic Architecture on the Redox Core Encapsulation
R. C. Pani, Y. G. Yingling
J. Phys. Chem. A 116 (2012) 7593-7599

35. X3DBio: A Visual Analysis Tool for Biomolecular Structure Exploration
H. Yi, A. Singh, Y. G. Yingling
Proc. SPIE 8294 (2012) 82940S-1-8

• • • Download X3DBio software

34. The role of hydrogen bonding in water-mediated glucose solubility in ionic liquids
H. S. Kim, R. Pani, S. H. Ha, Y.-M. Koo, Y. G. Yingling
Journal of Molecular Liquids 166 (2012) 25-30

33. Molecular dynamics simulaitons of bio-nano materials
M. A. Pasquinelli, Y. G. Yingling
Encyclopedia of Nanotechnology (2012) pp.1454-1463

32. Theoretical perspective on properties of DNA-functionalized surfaces
A. Singh, H. Eksiri, Y. G. Yingling
Journal of Polymer Science B: Polymer Physics 49 (2011) 1563-1627

• • • Cover Image

31. Interactions of cations with RNA loop-loop complexes
A. Singh, L. Sethaphong, Y. G. Yingling
Biophysical Journal 101 (2011) 727

• • • Cover Image

30. Simulations of stretching single stranded DNA
A. Singh, Y. G. Yingling
Mater. Res. Soc. Proc. (2011) 1301, mrsf10-1301-oo10-06 doi:10.1557/opl.2011.569.

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

• • • Reported in Materials360®, Foresight Institute

28. The sequence of HIV-1 TAR RNA helix controls cationic distribution
L. Sethaphong, A. Singh, A. E. Marlowe, Y. G. Yingling
J. Phys. Chem. C 114 (2010) 5506-5512

27. Comparing ion distributions around RNA and DNA helical and loop-loop motifs
A. V. Semichaevsky, A. E. Marlowe, Y. G. Yingling
Mater. Res. Soc. Symp. Proc. Vol. 1130 (2009) W05-05

26. A. Singh and Y. 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
27. 25. S. Snyder and Y. 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. The 3′ Proximal Translational Enhancer of Turnip Crinkle Virus Binds to 60S Ribosomal Subunits
V. A. Stupina, A. Meskauskas, J. C. Mccormack, Y. G. Yingling, B. A. Shapiro, J. D. Dinman, A. E. Simon
RNA 14 (2008) 2379-2393

23. Structural Domains Within the 3′ UTR of Turnip Crinkle Virus
J. C. McCormack, X. Yuan, Y. G. Yingling, W. Kasprzak, R. E. Zamora, B. A. Shapiro, A. E. Simon
Journal of Virology 82 (2008) 8706-8720

22. Protocols for the In silico Design of RNA Nanostructures
B. A. Shapiro, E. Bindewald, W. Kasprzak, Y. G. Yingling
Nanostructure Design Methods and Protocols, Methods in Molecular Biology series Vol. 474, E. Gazit and R. Nussinov, Eds., (Humana Press, 2008)

21. RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
E.Bindewald, R. Hayes, Y. G. Yingling, W. Kasprzak, B. A. Shapiro
Nucleic Acids Res. 36 (2008) D392-D397

• • • Link to RNAJunction database

20. Computational design of an RNA hexagonal nano-ring and an RNA nanotube
Y. G. Yingling, B. A. Shapiro
Nano Letters 7 (2007) 2328-2334

19. Bridging the gap in RNA structure prediction
B. A. Shapiro, Y. G. Yingling, W. Kasprzak, E. Bindewald
Current Opinion in Structural Biology 17 (2007) 157-165

18. Incorporation of chemical reactions into UV photochemical ablation of coarse-grained material
Y. G. Yingling, B. J. Garrison
Applied Surface Science 253 (2007) 6377-6381

17. Computational Investigation into the Mechanisms of UV Ablation of Poly (methyl methacrylate)
M. Prasad, P. F. Conforti, B. J. Garrison, Y. G. Yingling
Applied Surface Science 253 (2007) 6382-6385

16. The Impact of Dyskeratosis Congenita Mutations on Structure and Dynamics of the Telomerase RNA Pseudoknot Domain
Y. G. Yingling, B. A. Shapiro
J. Biomol. Str. Dynam. 24 (2007) 303-320

• • • Cover Image

15. Computational studies of ultraviolet ablation of poly(methyl methacrylate)
P. F. Conforti, Y. G. Yingling and B. J. Garrison
Journal of Physics: C 59 (2007) 322-327

14. The Prediction of the Wild-type Telomerase RNA Pseudoknot Structure and the Pivotal Role of a Bulge in its Formation
Y. G. Yingling, B. A. Shapiro
J Mol Graph Model 25 (2006) 261-274

13. Structural and Dynamical Classification of RNA Single-Base Bulges for Nanostructure Design
W. A. Hastings, Y. G. Yingling, G. S. Chirikjian, B. A. Shapiro
J Comp Theor Nanoscience 3 (2006) 63-77

12. Coarse-Grained Model of the Interaction of Light with Polymeric Material: Onset of Ablation
Y. G. Yingling, B. J. Garrison
Journal of Physical Chemistry B 109 (2005) 16482-16489

11. Dynamic Behavior of the Telomerase RNA Hairpin Structure and Its Relationship to Dyskeratosis Congenita
Y. G. Yingling, B. A. Shapiro
Journal of Molecular Biology 348 (2005) 27

10. Theoretical Investigation of Laser Pulse Width Dependence in Thermal Confinement Regime
Y. G. Yingling, P. F. Conforti, B. J. Garrison
Appl. Phys. A 79 (2004) 757

9. Coarse Grained Chemical Reaction Model
Y. G. Yingling and B. J. Garrison
J. Phys. Chem. B 108 (2004) 1815

• • • Feature Article

8. Photochemical Ablation of Organic Solids
Y. G. Yingling and B. J. Garrison
Nucl. Instrum. Methods Phys. Research B 203 (2003) 188

7. Computer Simulation of Laser Ablation of Molecular Substrates
L. V. Zhigilei, E. Leveugle, B. J. Garrison, Y. G. Yingling, M. I. Zeifman
Chemical Reviews 103 (2003) 321

6. MD Simulations of MALDesorption – Connections to Experiment
L. V. Zhigilei, Y. G. Yingling, T. E. Itina, T. A. Schoolcraft, B. J. Garrison
Int. J. Mass Spectrom. Ion Processes 226 (2003) 85

5. Big Molecule Ejection – SIMS vs. MALDI
B. J. Garrison, A. Delcorte, L. V. Zhigilei, T. E. Itina, K. D. Krantzman, Y. G. Yingling, C. M. McQuaw, E. J. Smiley, N. Winograd
Applied Surface Science 69-71 (2003) 203

4. Photochemical induced effects in material ejection in laser ablation
Y. G. Yingling and B. J. Garrison
Chem. Phys. Lett. 364 (2002) 237

3. The Role of the Photochemical Fragmentation in Laser Ablation
Y. G. Yingling, L. V. Zhigilei, B. J. Garrison
J. Photochemistry and Photobiology A: Chemistry 145 (2001) 173

2. Photochemical Fragmentation Processes in Laser Ablation of Organic Solids
Y. G. Yingling, L. V. Zhigilei, B. J. Garrison
Nucl. Instrun. Methods Phys. Research B 180 (2001) 171

1. Laser Ablation of bicomponent Systems: A Probe of Molecular Ejection Mechanisms
Y. G. Yingling, L. V. Zhigilei, B. J. Garrison, A. Koubenakis, J. Labrakis, S. Georgiou
Appl. Phys. Lett. 78 (2001) 1631