Publications

2016   2015   2014   2013   2012   2011   2010   2009   2008   prior to 2007

68. 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 (2017)
67. 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
66. 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
65. 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
64. 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

2016


63. 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
62. 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
61. Silk Fibroin-Substrate Interactions at Heterogeneous Nanocomposite Interfaces
A. M. Grant, Ho Shin Kim, Trisha L. Dupnock, K. Hu, Yaroslava G. Yingling, Vladimir V. Tsukruk
Advanced Functional Materials 26 (2016) 6380-6392
60. 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
59. 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 G. Vandavasi, Hugh O'Neill, Eric M. Roberts, Alison W. Roberts, Yaroslava G. Yingling, Candace H. Haigler
Scientific Reports 6 (2016) 28696
58. 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
57. 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 (2016) DOI: 10.1557/adv.2016.91
56. 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
55. 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
54. 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
53. 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

2015


52. 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
51. 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
50. 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
49. 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
48. 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
47. 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
46. 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.

2014


45. 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
44. 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.
43. 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.
42. 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.
41. 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.

2013


40. 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.
39. 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
38. 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 Access the recommendation on F1000Prime
37. 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

2012


36. 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
35. 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
34. 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
33. X3DBio: A Visual Analysis Tool for Biomolecular Structure Exploration
H. Yi, A. Singh, Y. G. Yingling
Proc. SPIE 8294 (2012) 82940S-1-8
32. 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
31. Molecular dynamics simulaitons of bio-nano materials
M. A. Pasquinelli, Y. G. Yingling
Encyclopedia of Nanotechnology (2012) pp.1454-1463

2011


30. 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
29. Interactions of cations with RNA loop-loop complexes
A. Singh, L. Sethaphong, Y. G. Yingling
Biophysical Journal 101 (2011) 727
28. 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.

2010


27. 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
26. 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

2009


25. 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

2008


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

2007


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
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

2006


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

2005


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

2004


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

2003


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

2002


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

2001


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

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