Education

Research Description

Research interests in Prof. Yingling’s group are focused on the development of advanced computational models and novel algorithms for multiscale molecular modeling of soft and biological materials and aim to provide a fundamental understanding of the structure-property relations of a variety of soft materials systems that are formed through the process of self-assembly.  Specifically, Dr. Yingling's research interests include multiscale molecular modeling and computer simulations of soft materials: polymers, biomolecules, nanoparticles, organic-inorganic composites; design and properties of nanomaterials; inorganic-organic interfaces and surfaces; biomolecular 3D structure prediction; effect of solvents and additives on materials properties; interactions between nanoparticles and bio and polymeric materials.

Honors and Awards

• University Faculty Scholar, North Carolina State University, 2014
• OpenEye Outstanding Junior Faculty Award from the ACS Computers in Chemistry (COMP) Division, 2012
• National Science Foundation CAREER Award, 2012
• NIH National Cancer Institute Center for Cancer Research exceptional stipend, 2007
• Best Ph.D. Thesis Award from the Materials Research Institute at Pennsylvania State University, 2003
• Braucher Fellowship for Graduate Student Research , 2002
• Miller Graduate Student Research Award , 2001

Publications

Bathophenanthroline Disulfonate Ligand-Induced Self-Assembly of Ir(III) Complexes in Water: An Intriguing Class of Photoluminescent Soft Materials

McGoorty, M. M., Singh, A., Deaton, T. A., Peterson, B., Taliaferro, C. M., Yingling, Y. G., & Castellano, F. N. (2018), ACS OMEGA, 3(10), 14027–14038. https://doi.org/10.1021/acsomega.8b02034

Cellulose synthase "class specific regions' are intrinsically disordered and functionally undifferentiated

Scavuzzo-Duggan, T. R., Chaves, A. M., Singh, A., Sethaphong, L., Slabaugh, E., Yingling, Y. G., … Roberts, A. W. (2018). Cellulose synthase "class specific regions’ are intrinsically disordered and functionally undifferentiated. Journal of Integrative Plant Biology, 60(6), 481–497. https://doi.org/10.1111/jipb.12637,

Functional modification of silica through enhanced adsorption of elastin-like polypeptide block copolymers

Li, L. Y., Li, N. K., Tu, Q., Im, O., Mo, C. K., Han, W., … Lopez, G. P. (2018), Biomacromolecules, 19(2), 298–306.

Interfacial stability of graphene-based surfaces in water and organic solvents

Kim, H., Oweida, T. J., & Yingling, Y. G. (2018), Journal of Materials Science, 53(8), 5766–5776.

Progress in ligand design for monolayer-protected nanoparticles for nanobio interfaces

Manning, M. D., Kwansa, A. L., Oweida, T., Peerless, J. S., Singh, A., & Yingling, Y. G. (2018), BIOINTERPHASES, 13(6). https://doi.org/10.1116/1.5044381

Sequence directionality dramatically affects lcst behavior of elastin-like polypeptides

Li, N. K., Roberts, S., Quiroz, F. G., Chilkoti, A., & Yingling, Y. G. (2018), Biomacromolecules, 19(7), 2496–2505.

Wrapping nanocellulose nets around graphene oxide sheets

Xiong, R., Kim, H. S., Zhang, L. J., Korolovych, V. F., Zhang, S. D., Yingling, Y. G., & Tsukruk, V. V. (2018), Angewandte Chemie [International Edition in English], 57(28), 8508–8513.

Advances in molecular modeling of nanoparticle nucleic acid interfaces

Nash, J. A., Kwansa, A. L., Peerless, J. S., Kim, H. S., & Yingling, Y. G. (2017), Bioconjugate Chemistry, 28(1), 3–10.

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

Kim, H. S., Farmer, B. L., & Yingling, Y. G. (2017), Advanced Materials Interfaces, 4(8).

Interfacial mechanical properties of graphene on self-assembled monolayers: Experiments and simulations

Tu, Q., Kim, H. S., Oweida, T. J., Parlak, Z., Yingling, Y. G., & Zauscher, S. (2017), ACS Applied Materials & Interfaces, 9(11), 10203–10213.

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

Li, N. K., Kuang, H., Fuss, W. H., Zauscher, S., Kokkoli, E., & Yingling, Y. G. (2017), Macromolecular Rapid Communications, 38(20).

Template-guided assembly of silk fibroin on cellulose nanofibers for robust nanostructures with ultrafast water transport

Xiong, R., Kim, H. S., Zhang, S. D., Kim, S., Korolovych, V. F., Ma, R. L., … Tsukruk, V. V. (2017), ACS Nano, 11(12), 12008–12019.

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

Nash, J. A., Tucker, T. L., Therriault, W., & Yingling, Y. G. (2016), Biointerphases, 11(4).

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

Nixon, B. T., Mansouri, K., Singh, A., Du, J., Davis, J. K., Lee, J. G., … Haigler, C. H. (2016), Scientific Reports, 6. https://doi.org/10.1038/srep28696

Design of potent and controllable anticoagulants using dna aptamers and nanostructures

Rangnekar, A., Nash, J. A., Goodfred, B., Yingling, Y. G., & LaBean, T. H. (2016), Molecules, 21(2).

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

Ge, W. Y., Li, N. K., McCormick, R. D., Lichtenberg, E., Yingling, Y. G., & Stiff-Roberts, A. D. (2016), ACS Applied Materials & Interfaces, 8(30), 19494–19506.

Fluorescence blinking as an output signal for biosensing

Roark, B., Tan, J. A., Ivanina, A., Chandler, M., Castaneda, J., Kim, H. S., … Afonin, K. A. (2016), ACS Sensors, 1(11), 1295–1300.

LCST behavior is manifested in a single molecule: Elastin-like polypeptide (VPGVG)n

Zhao, B. W., Li, N. K., Yingling, Y. G., & Hall, C. K. (2016), Biomacromolecules, 17(1), 111–118.

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

Sethaphong, L., Davis, J. K., Slabaugh, E., Singh, A., Haigler, C. H., & Yingling, Y. G. (2016), Cellulose, 23(1), 145–161. https://doi.org/10.1007/s10570-015-0789-6

Sequence dependent interaction of single stranded DNA with graphitic flakes: Atomis molecular dynamics simulations

Kim, H. S., Huang, S. M., & Yingling, Y. C. (2016), MRS Advances, 1(25), 1883–1889.

Silk fibroin-substrate interactions at heterogeneous nanocomposite interfaces

Grant, A. M., Kim, H. S., Dupnock, T. L., Hu, K., Yingling, Y. G., & Tsukruk, V. V. (2016), Advanced Functional Materials, 26(35), 6380–6392.

A barley efflux transporter operates in a Na+-dependent manner, as revealed by a multidisciplinary platform

Nagarajan, Y., Rongala, J., Luang, S., Singh, A., Shadiac, N., Hayes, J., … Hrmovaa, M. (2016), Plant Cell, 28(1), 202–218.

The effect of imidazolium cations on the structure and activity of the Candida antarctica Lipase B enzyme in ionic liquids

Kim, H. S., Eom, D., Koo, Y. M., & Yingling, Y. G. (2016), Physical Chemistry Chemical Physics, 18(32), 22062–22069.

CELLULOSE SYNTHASE INTERACTIVE1 is required for fast recycling of cellulose synthase complexes to the plasma membrane in arabidopsis

Lei, L., Singh, A., Bashline, L., Li, S. D., Yingling, Y. G., & Gu, Y. (2015), Plant Cell, 27(10), 2926–2940.

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

Nash, J. A., Singh, A., Li, N. K., & Yingling, Y. G. (2015), ACS Nano, 9(12), 12374–12382.

Fullerenes in aromatic solvents: correlation between solvation-shell structure, solvate formation, and solubility

Peerless, J. S., Bowers, G. H., Kwansa, A. L., & Yingling, Y. G. (2015), Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 119(49), 15344–15352.

How cellulose elongates-A QM/MM study of the molecular mechanism of cellulose polymerization in bacterial CESA

Yang, H., Zimmer, J., Yingling, Y. G., & Kubicki, J. D. (2015), Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 119(22), 6525–6535.

Microtubules and cellulose biosynthesis: The emergence of new players

Li, S. D., Lei, L., Yingling, Y. G., & Gu, Y. (2015), Current Opinion in Plant Biology, 28, 76–82.

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

Li, N. K., Fuss, W. H., Tang, L., Gu, R. P., Chilkoti, A., Zauscher, S., & Yingling, Y. G. (2015), Soft Matter, 11(42), 8236–8245.

An Implicit solvent ionic strength (ISIS) method to model polyelectrolyte systems with dissipative particle dynamics

Li, N. K., Fuss, W. H., & Yingling, Y. G. (2015), Macromolecular Theory and Simulations, 24(1), 7–12.

Cellulose synthases: new insights from crystallography and modeling

Slabaugh, E., Davis, J. K., Haigler, C. H., Yingling, Y. G., & Zimmer, J. (2014), Trends in Plant Science, 19(2), 99–106. https://doi.org/10.1016/j.tplants.2013.09.009

Computational and genetic evidence that different structural conformations of a non-catalytic region affect the function of plant cellulose synthase

Slabaugh, E., Sethaphong, L., Xiao, C. W., Amick, J., Anderson, C. T., Haigler, C. H., & Yingling, Y. G. (2014), Journal of Experimental Botany, 65(22), 6645–6653. https://doi.org/10.1093/jxb/eru383

Enzymatic polymerization of high molecular weight DNA amphiphiles that self-assemble into star-like micelles

Tang, L., Tjong, V., Li, N., Yingling, Y. G., Chilkoti, A., & Zauscher, S. (2014), Advanced Materials, 26(19), 3050–3054.

Molecular description of the LCST behavior of an elastin-like polypeptide

Li, N. K., Quiroz, F. G., Hall, C. K., Chilkoti, A., & Yingling, Y. G. (2014), Biomacromolecules, 15(10), 3522–3530.

Progress in molecular modelling of DNA materials

Li, N. K., Kim, H. S., Nash, J. A., Lim, M., & Yingling, Y. G. (2014), Molecular Simulation, 40(10-11), 777–783.

The relationship between enhanced enzyme activity and structural dynamics in ionic liquids: a combined computational and experimental study

Kim, H. S., Ha, S. H., Sethaphong, L., Koo, Y. M., & Yingling, Y. G. (2014), Physical Chemistry Chemical Physics, 16(7), 2944–2953.

Correlating fullerene diffusion with the polythiophene morphology: Molecular dynamics simulations

Pani, R. C., Bond, B. D., Krishnan, G., & Yingling, Y. G. (2013), Soft Matter, 9(42), 10048–10055.

Tertiary model of a plant cellulose synthase

Sethaphong, L., Haigler, C. H., Kubicki, J. D., Zimmer, J., Bonetta, D., DeBolt, S., & Yingling, Y. G. (2013), Proceedings of the National Academy of Sciences of the United States of America, 110(18), 7512–7517. https://doi.org/10.1073/pnas.1301027110

X3DBio2: A visual analysis tool for biomolecular structure comparison

Yi, H., Thakur, S., Sethaphong, L., & Yingling, Y. G. (2013), Proceedings of SPIE-the International Society for Optical Engineering, 8654, 86540W.

Role of solvent and dendritic architecture on the redox core encapsulation

Pani, R. C., & Yingling, Y. G. (2012), Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment & General Theory, 116(28), 7593–7599.

Weakly charged cationic nanoparticles induce DNA bending and strand separation

Railsback, J. G., Singh, A., Pearce, R. C., McKnight, T. E., Collazo, R., Sitar, Z., … Melechko, A. V. (2012), Advanced Materials, 24(31), 4261–.

X3DBio1: a visual analysis tool for biomolecular structure exploration

Yi, H., Singh, A., & Yingling, Y. G. (2012), Proceedings of SPIE-the International Society for Optical Engineering, 8294, 8294OS.

The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study

Marlowe, A. E., Singh, A., & Yingling, Y. G. (2012), Materials Science & Engineering. C, Biomimetic Materials, Sensors and Systems, 32(8), 2583–2588.

The role of hydrogen bonding in water-mediated glucose solubility in ionic liquids

Kim, H. S., Pani, R., Ha, S. H., Koo, Y. M., & Yingling, Y. G. (2012), Journal of Molecular Liquids, 166, 25–30.

Interactions of cations with RNA loop-loop complexes

Singh, A., Sethaphong, L., & Yingling, Y. G. (2011), Biophysical Journal, 101(3), 727–735.

Theoretical perspective on properties of DNA-functionalized surfaces

Singh, A., Eksiri, H., & Yingling, Y. G. (2011), Journal of Polymer Science. Part B, Polymer Physics, 49(22), 1563–1568.

Effect of oligonucleotide length on the assembly of DNA materials: Molecular dynamics simulations of layer-by-layer DNA films

Singh, A., Snyder, S., Lee, L., Johnston, A. P. R., Caruso, F., & Yingling, Y. G. (2010), Langmuir, 26(22), 17339–17347.

The Sequence of HIV-1 TAR RNA helix controls cationic distribution

Sethaphong, L., Singh, A., Marlowe, A. E., & Yingling, Y. G. (2010), Journal of Physical Chemistry. C, 114(12), 5506–5512.

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Grants

NextGen Fellowship – Accelerating Materials Science and Educating the​ ​Next​ Generation​ ​of​ ​Scientists​ ​and​ Engineers

Schmidt Family Foundation(5/01/18 - 9/30/18)

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NextGen Fellowship – Accelerating Materials Science and Educating the​ ​Next​ Generation​ ​of​ ​Scientists​ ​and​ Engineers

Sponsor: Schmidt Family Foundation

Start Date: 5/01/18

End Date: 9/30/18

Abstract

Impact​ ​on​ ​communities​ ​involved​ ​-​ ​what​ ​will​ ​have​ ​changed​ ​as​ ​a​ ​result After the NextGen Fellowship: 1. University research labs will adopt machine learning into their workflows, accelerating the pace of scientific discovery 2. Research performed by NextGen fellows and their groups will become the gold standard for impactful data-driven research in the materials community. 3. NextGen fellows will act as evangelists that encourage future students and researchers to embrace data management best practices. Reaching these three impact goals will promote the widespread adoption to the point where every academic group developing new materials at the top 100 research universities will have a NextGen researcher. Furthermore, this program will foster a much-needed culture of open sourced data in the materials science community.

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Heteroaggregation for Nanomanufacturing and Magnetic Alignment of Multifunctional Nanoparticles

National Science Foundation (NSF)(6/01/18 - 5/31/21)

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Heteroaggregation for Nanomanufacturing and Magnetic Alignment of Multifunctional Nanoparticles

Sponsor: National Science Foundation (NSF)

Start Date: 6/01/18

End Date: 5/31/21

Abstract

This proposal is to study the use of heteroaggregation as a simple method for assembly of multifunctional nanoparticles.

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Collaborative Research: Design Principles for Multi-functional Polymer Dispersion Blends

National Science Foundation (NSF)(8/01/17 - 7/31/20)

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Collaborative Research: Design Principles for Multi-functional Polymer Dispersion Blends

Sponsor: National Science Foundation (NSF)

Start Date: 8/01/17

End Date: 7/31/20

Abstract

Polymer dispersions are a general class of materials in which fine (nano- and micro-sized) polymeric particles are dispersed in an aqueous phase. Such materials are commonly used in several industries, including medicine, paints and coatings, automobiles, and plastics. The application of polymer dispersions to emerging technologies, such as organic optoelectronic devices (e.g., solar cells, light emitting diodes, or photodetectors), could take advantage of existing industrial infrastructure to help catapult polymer dispersions into the consumer electronics market. This potential new application area poses a significant challenge for traditional polymer dispersions because of the great diversity of organic materials that constitute optoelectronic devices. In addition, a priori predictions of the structure of polymer dispersions and the resultant film properties are extremely difficult due to known correlations that exist among constituent material properties, emulsion processing parameters, polymer dispersion structure/morphology, thin-film deposition parameters, and film properties. This challenge is exacerbated by the mesoscale nature of the material system that prevents application of first-principles theoretical approaches. As a result, it is difficult to design a polymer dispersion that will yield specified film characteristics. Therefore, the overall goal of the proposed work is to establish fundamental process-structure-property relationships to guide the predictive design of a new class of polymer dispersions applicable to organic optoelectronic devices.

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Composite Packed-Bed Nanofiltration for High-throughput Desalination

NCSU Water Resources Research Institute(9/01/16 - 8/31/17)

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Composite Packed-Bed Nanofiltration for High-throughput Desalination

Sponsor: NCSU Water Resources Research Institute

Start Date: 9/01/16

End Date: 8/31/17

Abstract

U.S. municipal water sources have been increasingly dependent on desalination processes for clean water, yet in North Carolina critical water quality and economic issues have arisen with desalination processes. We propose herein to utilize efficient computational methods to design and characterize a novel packed-bed filter construction for the filtration and desalination of brackish groundwater.

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EMN-14-S-S-05 Modeling of Diffusion of Additive Compounds in Rubber

Eastman Chemical Company(11/30/-1 - 10/31/17)

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EMN-14-S-S-05 Modeling of Diffusion of Additive Compounds in Rubber

Sponsor: Eastman Chemical Company

Start Date: 11/30/-1

End Date: 10/31/17

Abstract

Confidential

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Wetting of Patterned Silicon Surfaces

Eastman Chemical Company(1/01/14 - 8/01/14)

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Wetting of Patterned Silicon Surfaces

Sponsor: Eastman Chemical Company

Start Date: 1/01/14

End Date: 8/01/14

Abstract

Modeling of solvent surface interactions.

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Center For Lignocellulose Structure and Formation

US Dept. of Energy (DOE)(8/01/14 - 7/31/19)

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Center For Lignocellulose Structure and Formation

Sponsor: US Dept. of Energy (DOE)

Start Date: 8/01/14

End Date: 7/31/19

Abstract

This proposal is a revised renewal proposal for the Center for Lignocellulose Structure and Formation. Bridging three Colleges at NC State (CALS, COE, CNR) and two disciplines, the research in the renewal phase will be directed toward understanding and manipulating the structure of plant cell walls. The work will include plant genetics, biotechnology, and computational modeling of protein structure. The research has relevance to the improvement of cellulosic renewable biomaterials and biomass feedstocks, such as those used in biofuels production.

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Confinement, Dynamics, and Orientation of DNA at Nano-interfaces

National Science Foundation (NSF)(7/01/14 - 6/30/18)

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Confinement, Dynamics, and Orientation of DNA at Nano-interfaces

Sponsor: National Science Foundation (NSF)

Start Date: 7/01/14

End Date: 6/30/18

Abstract

The main research objective of this collaborative project that combines experimental and theoretical efforts is to attain a fundamental understanding of effects of nano-confinement on dynamics, orientation, and conformations of DNA upon electrostatic binding to nanostructures of convex and concave shapes. We aim at integrating experimental and theoretical modelling efforts. Experimentally, Smirnov group will 1) fabricate both convex (ligand protected Au nanoparticles) and concave (ligand modified nanopores) nanostructures and 2) characterize structure, dynamics, electrostatics of the ligands and conformations of DNA with spin-labeling EPR methods. Collaborating Yingling group will 3) carry out atomistic-level molecular dynamics (MD) simulations of the organic ligand shell upon interactions with DNA to predict various binding modes (second order phase transitions) that will be verified experimentally. Taken together, these studies will provide for fundamental knowledge of DNA-nano-interface and nano-confinement effects, thus, enabling further development of nano-biosensors, DNA-based materials, and novel approaches for gene therapy.

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Collaborative Research: Supramolecular Materials by Nucleic Acid Block Copolymer Self-Assembly

National Science Foundation (NSF)(7/15/14 - 6/30/18)

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Collaborative Research: Supramolecular Materials by Nucleic Acid Block Copolymer Self-Assembly

Sponsor: National Science Foundation (NSF)

Start Date: 7/15/14

End Date: 6/30/18

Abstract

The overall goal of this interdisciplinary, collaborative research proposal is to design and synthesize polynucleotide copolymers with chemical functionalities that drive solution self-assembly into micelles and that harness DNA’s molecular recognition properties to create oriented, supramolecular nano- and mesostructures over large areas on surfaces.

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Modeling Lipase Variants

Eastman Chemical Company(11/01/13 - 12/01/15)

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Modeling Lipase Variants

Sponsor: Eastman Chemical Company

Start Date: 11/01/13

End Date: 12/01/15

Abstract

Confidential

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