Yaroslava G Yingling

Also known as: Yara Yingling

computational materials science

Works (155)

Updated: May 15th, 2024 06:10

2024 journal article

Electrostatic self-assembly yields a structurally stabilized PEDOT:PSS with efficient mixed transport and high-performance OECTs

MATTER, 7(3).

By: L. Taussig n, M. Ghasemi n, S. Han*, A. Kwansa n, R. Li*, S. Keene*, N. Woodward n, Y. Yingling n ...

UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 22, 2024

2024 article

Monomer Architecture as a Mechanism to Control the Self-Assembly of Oligomeric Diblock Peptide-Polymer Amphiphiles

Allen, B., Pinky, S., Beard, E., Calzadilla, N., Gringeri, A., Sanders, M., … Yingling, Y. (2024, April 8).

By: B. Allen*, S. Pinky n, E. Beard*, N. Calzadilla*, A. Gringeri*, M. Sanders*, A. Knight*, Y. Yingling n

Source: ORCID
Added: April 15, 2024

2024 article

Monomer Architecture as a Mechanism to Control the Self-Assembly of Oligomeric Diblock Peptide-Polymer Amphiphiles

Allen, B., Pinky, S., Beard, E., Gringeri, A., Calzadilla, N., Sanders, M., … Knight, A. (2024, April 9).

By: B. Allen*, S. Pinky n, E. Beard*, A. Gringeri*, N. Calzadilla*, M. Sanders*, Y. Yingling n, A. Knight*

Source: ORCID
Added: April 15, 2024

2024 article

Phosphate-binding protein-loaded iron oxide particles: adsorption performance for phosphorus removal and recovery from water

Hussein, F. B., Cannon, A. H., Hutchison, J. M., Gorman, C. B., Yingling, Y. G., & Mayer, B. K. (2024, March 28). ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY, Vol. 3.

By: F. Hussein, A. Cannon*, J. Hutchison, C. Gorman*, Y. Yingling* & B. Mayer

Sources: ORCID, Web Of Science, NC State University Libraries
Added: April 8, 2024

2024 article

Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods

Kwansa, A. L., Singh, A., Williams, J. T., Haigler, C. H., Roberts, A. W., & Yingling, Y. G. (2024, January 6). CELLULOSE, Vol. 1.

By: A. Kwansa n, A. Singh n, J. Williams n, C. Haigler n, A. Roberts* & Y. Yingling n

author keywords: Plant cellulose synthesis; Protein homology model; Molecular dynamics simulation; Hydrogen bonding; Gossypium hirsutum
Sources: Web Of Science, NC State University Libraries
Added: January 16, 2024

2023 article

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

Zhang, B., Pinky, S. K., Kwansa, A. L., Ferguson, S., Yingling, Y. G., & Stiff-Roberts, A. D. (2023, March 29). ACS APPLIED MATERIALS & INTERFACES, Vol. 3.

By: B. Zhang*, S. Pinky n, A. Kwansa n, S. Ferguson*, Y. Yingling n & A. Stiff-Roberts*

author keywords: matrix-assisted pulsed laser evaporation; molecular dynamics; polyfluorene; emulsions; light-emitting diodes
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
Added: March 30, 2023

2023 journal article

DFT-Based Calculation of Molecular Hyperpolarizability and SFG Intensity of Symmetric and Asymmetric Stretch Modes of Alkyl Groups

JOURNAL OF PHYSICAL CHEMISTRY B, 127(39), 8456–8467.

By: J. Choi*, A. Kwansa n, Y. Yingling n & S. Kim*

UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries, ORCID
Added: October 16, 2023

2023 article

Effect of solvent on the emulsion and morphology of polyfluorene films: all-atom molecular dynamics approach

Pinky, S. K., Kwansa, A. L., Zhang, B., Stiff-Roberts, A. D., & Yingling, Y. G. (2023, February 2). SOFT MATTER, Vol. 2.

By: S. Pinky n, A. Kwansa n, B. Zhang*, A. Stiff-Roberts* & Y. Yingling n

UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 14, 2023

2023 journal article

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

STRUCTURE, 31(10), 1166-+.

By: P. Verma*, A. Kwansa n, R. Ho*, Y. Yingling n & J. Zimmer*

TL;DR: Substrate- and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar) are presented and prolonged interactions of the gating loop with the substrate molecule, particularly across its central conserved region are revealed. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: November 13, 2023

2023 article

Molecular Mechanism of Plasticizer Exudation from Polyvinyl Chloride

Kwansa, A. L. L., Pani, R. C. C., DeLoach, J. A. A., Tieppo, A., Moskala, E. J. J., Perri, S. T. T., & Yingling, Y. G. G. (2023, June 22). MACROMOLECULES, Vol. 6.

By: A. Kwansa n, R. Pani n, J. DeLoach*, A. Tieppo*, E. Moskala*, S. Perri*, Y. Yingling n

Sources: Web Of Science, NC State University Libraries, ORCID
Added: July 10, 2023

2023 article

Resolving Structure of ssDNA in Solution by Fusing Molecular Simulations and Scattering Experiments with Machine Learning

Oweida, T. J., & Yingling, Y. G. (2023, September 7). ADVANCED THEORY AND SIMULATIONS, Vol. 9.

By: T. Oweida n & Y. Yingling n

author keywords: flexible molecular structure determination; genetic algorithm; molecular dynamics simulations; SAXS; ssDNA
TL;DR: The results are able to determine the most accurate atomistic representation of poly‐Thymine (polyT) in solution to date that closely matches the experimental SAXS observations enabling a better understanding of the behavior of ssDNA in solution. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 18, 2023

2023 article

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

Peerless, J. S., Gulyuk, A. V., Milliken, N. J. B., Kim, G. D., Reid, E., Lee, J. W., … Yingling, Y. G. (2023, January 25). ACS ES&T WATER, Vol. 1.

By: J. Peerless n, A. Gulyuk n, N. Milliken n, G. Kim*, E. Reid*, J. Lee*, D. Kim*, Z. Hendren*, Y. Choi*, Y. Yingling n

author keywords: solvent-based desalination; organic solvent; molecular dynamics simulation; temperature swing solvent extraction
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (Web of Science; OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 27, 2023

2023 article

Solvent Effects in Ligand Stripping Behavior of Colloidal Nanoparticles

Mahmood, A. U., Rizvi, M. H., Tracy, J. B., & Yingling, Y. G. (2023, June 13). ACS NANO, Vol. 6.

By: A. Mahmood n, M. Rizvi n, J. Tracy n & Y. Yingling n

author keywords: nanoparticles; atomisticsimulations; ligandremoval; ligand stripping isotherm; solvent effects
Sources: Web Of Science, NC State University Libraries, ORCID
Added: July 3, 2023

2023 article

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

Chatterjee, A., Pratakshya, P., Kwansa, A. L., Kaimal, N., Cannon, A. H., Sartori, B., … Gorodetsky, A. A. (2023, January 24). ACS BIOMATERIALS SCIENCE & ENGINEERING, Vol. 1.

By: A. Chatterjee*, P. Pratakshya*, A. Kwansa n, N. Kaimal*, A. Cannon n, B. Sartori*, B. Marmiroli*, H. Orins* ...

author keywords: cephalopods; engineered cells; optical materials; refractive index; self-assembly; proteins; reflectins
MeSH headings : Animals; Decapodiformes / chemistry; Refractometry; Proteins / chemistry; Biocompatible Materials; Nanostructures
TL;DR: A synergistic combination of experimental and computational methodologies are employed to systematically map the three-dimensional refractive index distributions of model self-assembled reflectin-based structures both in vivo and in vitro and may improve understanding of squid skin cell functionality, augment existing methods for characterizing protein-based optical materials, and expand the utility of emerging holotomographic microscopy techniques. (via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
14. Life Below Water (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 13, 2023

2022 journal article

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

Physchem.

By: Y. Xie n, N. Li n, A. Singh n, S. Deshmukh* & Y. Yingling n

UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Source: ORCID
Added: March 23, 2022

2022 journal article

All-Atom Simulation Method for Zeeman Alignment and DipolarAssembly of Magnetic Nanoparticles br

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 18(5), 3122–3135.

By: A. Mahmood n & Y. Yingling n

MeSH headings : Ligands; Magnetic Fields; Magnetics; Magnetite Nanoparticles / chemistry; Solvents
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
Added: March 11, 2022

2022 article

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

Du, J., Vandavasi, V. G., Molloy, K. R., Yang, H., Massenburg, L. N., Singh, A., … Nixon, B. T. (2022, August 10). BIOMACROMOLECULES, Vol. 8.

By: J. Du*, V. Vandavasi*, K. Molloy*, H. Yang*, L. Massenburg*, A. Singh n, A. Kwansa n, Y. Yingling n ...

MeSH headings : Arabidopsis / genetics; Arabidopsis Proteins; Cell Wall; Cellulose; Glucosyltransferases / chemistry; Glucosyltransferases / genetics
TL;DR: Inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD suggest that homomeric CESA trimers may be important for the synthesis of primary and secondary cell walls and identify key residues for future mutagenic studies. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: August 11, 2022

2022 journal article

Gold nanoparticle design for RNA compaction

BIOINTERPHASES, 17(6).

By: J. Nash n, M. Manning n, A. Gulyuk n, A. Kuznetsov* & Y. Yingling n

MeSH headings : Gold / chemistry; RNA; Metal Nanoparticles / chemistry; Ligands; Nucleic Acids / metabolism
TL;DR: Large-scale all-atom molecular dynamics simulations are used to show that correlations between ligand length, metal core size, and ligand excess free volume control the ability of nanoparticles to bend dsRNA far below its persistence length. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: November 3, 2022

2022 article

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

Allen, B. P., Wright, Z. M., Taylor, H. F., Oweida, T. J., Kader-Pinky, S., Patteson, E. F., … Knight, A. S. (2022, January 27). ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, Vol. 1.

By: B. Allen*, Z. Wright*, H. Taylor*, T. Oweida n, S. Kader-Pinky n, E. Patteson*, K. Bucci*, C. Cox* ...

author keywords: Biomimetic; Electron Microscopy; Peptide-Polymer Amphiphile; Self-Assembly; Supramolecular Chemistry
MeSH headings : Biomimetics; Hydrophobic and Hydrophilic Interactions; Particle Size; Peptides / chemistry; Polymers / chemistry
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 27, 2022

2022 journal article

Mapping the Morphological Landscape of Oligomeric Di‐block Peptide–Polymer Amphiphiles**

Angewandte Chemie.

By: B. Allen*, Z. Wright*, H. Taylor*, T. Oweida n, S. Kader‐Pinky n, E. Patteson*, K. Bucci*, C. Cox* ...

Source: ORCID
Added: January 27, 2022

2021 journal article

Assessment of AMBER Force Fields for Simulations of ssDNA

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 17(2), 1208–1217.

By: T. Oweida n, H. Kim n, J. Donald n, A. Singh n & Y. Yingling n

MeSH headings : DNA, Single-Stranded / chemistry; Fluorescence Resonance Energy Transfer; Models, Chemical; Nuclear Magnetic Resonance, Biomolecular / methods; Nucleic Acid Conformation; Scattering, Small Angle; X-Ray Diffraction
TL;DR: Assessment of existing Amber force fields for all-atom simulations of ssDNA in implicit and explicit solvents finds that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 15, 2021

2021 journal article

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

ACS APPLIED MATERIALS & INTERFACES, 13(33), 39030–39041.

By: M. Chandler*, B. Minevich*, B. Roark*, M. Viard*, M. Johnson*, M. Rizvi n, T. Deaton n, S. Kozlov* ...

author keywords: quantum dots; therapeutic nucleic acids; 3D assemblies; programmable assembly; materials organization; bioimaging; therapeutic delivery
MeSH headings : Cell Line, Tumor; Cell Membrane Permeability; Cell Survival / drug effects; Cell Tracking; Cross-Linking Reagents / chemistry; Drug Carriers / chemistry; Gene Silencing / drug effects; Humans; Luminescent Agents / chemistry; Models, Molecular; Nucleic Acids / chemistry; Optical Imaging; Quantum Dots / chemistry; Structure-Activity Relationship; Surface Properties
TL;DR: The programmability and intracellular activity of QD assemblies offer a strategy for nucleic acids to imbue the structure and therapeutic function into the formation of complex networks of nanostructures, while the photoluminescent properties of the material allow for optical tracking in cells in vitro. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 27, 2021

2021 journal article

Insights into Structure and Aggregation Behavior of Elastin-like Polypeptide Coacervates: All-Atom Molecular Dynamics Simulations

JOURNAL OF PHYSICAL CHEMISTRY B, 125(30), 8627–8635.

By: N. Li n, Y. Xie n & Y. Yingling n

MeSH headings : Elastin; Hydrophobic and Hydrophilic Interactions; Molecular Dynamics Simulation; Peptides; Temperature
TL;DR: All-atom molecular dynamics simulations of 27 90-mer ELPs in explicit water at 350 K provide an insight into the sequence-dependent structure of coacervates and molecular behavior of individual peptides during aggregation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 23, 2021

2021 journal article

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(8).

By: J. Burris n, M. Makarem*, E. Slabaugh n, A. Chaves*, E. Pierce n, J. Lee*, S. Kiemle*, A. Kwansa n ...

author keywords: AtCesA7; cellulose synthesis complex; genetic complementation; irx3-1 mutant; PpCesA5; protein engineering; sum frequency generation spectroscopy
TL;DR: The cumulative results show that the FTVTxK region is important for the function of an angiosperm secondary wall CesA as well as widely divergent primary wall CesAs, while differences in complementation results between isomers may reflect functional differences that can be explored in further work. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: August 6, 2021

2021 journal article

Uncertainty Quantification and Sensitivity Analysis of Partial Charges on Macroscopic Solvent Properties in Molecular Dynamics Simulations with a Machine Learning Model

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 61(4), 1745–1761.

By: J. Peerless n, A. Kwansa n, B. Hawkins n, R. Smith n & Y. Yingling n

MeSH headings : Machine Learning; Molecular Dynamics Simulation; Solvents; Static Electricity; Uncertainty
TL;DR: The results indicate that the effect of partial charge variance on bulk properties, such as solubility parameters, diffusivity, dipole moment, and density, measured from MD simulations is significant; however, measured properties are observed to be less sensitive to partial charges of less accessible atoms. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
Added: March 18, 2021

2021 journal article

Weakly Ionically Bound Thermosensitive Hyperbranched Polymers

LANGMUIR, 37(9), 2913–2927.

By: H. Lee*, A. Stryutsky*, A. Mahmood n, A. Singh n, V. Shevchenko, Y. Yingling n, V. Tsukruk*

TL;DR: It is suggested that, in contrast to traditional branched polymers, ionically linked PNIPAM macrocations can reversibly disassociate from the sulfonate groups and form mobile coronas, endowing the dynamic micellar morphologies. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 12, 2021

2020 journal article

Anisotropic Optical and Frictional Properties of Langmuir-Blodgett Film Consisting of Uniaxially-Aligned Rod-Shaped Cellulose Nanocrystals

ADVANCED MATERIALS INTERFACES, 7(9).

author keywords: cellulose nanocrystals; frictional anisotropy; Langmuir-Blodgett films; optical anisotropy; uniaxial alignments
Sources: Web Of Science, NC State University Libraries
Added: June 1, 2020

2020 journal article

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

ACS Applied Materials & Interfaces, 12(31), 35345–35353.

By: R. Xiong*, A. Singh n, S. Yu*, S. Zhang*, H. Lee*, Y. Yingling n, D. Nepal*, T. Bunning*, V. Tsukruk*

author keywords: mixed nanocelluloses; photonic films; self-assembly at interfaces; chiral nematic nanostructures; robust mechanical properties
MeSH headings : Cellulose / chemistry; Nanofibers / chemistry; Nanoparticles / chemistry; Particle Size; Polysaccharides / chemistry; Surface Properties
TL;DR: This study provides a novel strategy to transform the wood pulp residues into high-value-added photonic-bound polysaccharide materials that can overcome the conflicting trends in designing balanced mechanical and optical performance of chiral biofilms and their conversion to robust chiral photonic materials with enhanced performance. (via Semantic Scholar)
Source: ORCID
Added: July 23, 2020

2020 journal article

Effect of Octadecylamine Surfactant on DNA Interactions with Graphene Surfaces

Langmuir, 36(4), 931–938.

By: H. Kim n, N. Brown n, S. Zauscher* & Y. Yingling n

MeSH headings : Amines / chemistry; DNA / chemistry; Graphite / chemistry; Molecular Dynamics Simulation; Particle Size; Surface Properties; Surface-Active Agents / chemistry
TL;DR: All-atom molecular dynamics simulations to understand how various 1-octadecylamine coatings of graphene surface affect the conformation of double-stranded (dsDNA) on the surface concluded that both DNA sequence and ODA concentration play an essential role in experimentally observed conformational changes of DNA on the graphene surface. (via Semantic Scholar)
Source: ORCID
Added: January 23, 2020

2020 journal article

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

Cellulose, 27(10), 5597–5616.

By: A. Singh n, A. Kwansa n, H. Kim n, J. Williams n, H. Yang*, N. Li n, J. Kubicki*, A. Roberts*, C. Haigler n, Y. Yingling n

author keywords: Plant; Cellulose synthesis complex; Homotrimer; Protein structure prediction; Molecular dynamics simulation
TL;DR: A 3D atomic-resolution model of a full-length cotton CESA (GhCESA1) structure is presented that indicates that there are similarities to BcsA bacterial cellulose synthase, such as the transmembrane topology and the internalization of conserved catalytic motifs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: ORCID, Crossref, NC State University Libraries
Added: May 1, 2020

2020 article

Materials matter in phosphorus sustainability

Jones, J. L., Yingling, Y. G., Reaney, I. M., & Westerhoff, P. (2020, January). MRS BULLETIN, Vol. 45, pp. 7–10.

By: J. Jones n, Y. Yingling n, I. Reaney* & P. Westerhoff*

UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: February 17, 2020

2020 journal article

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

MRS Advances, 3, 1–18.

By: T. Oweida n, A. Mahmood n, M. Manning n, S. Rigin n & Y. Yingling n

author keywords: education; informatics; material availability; data
TL;DR: The growing use of materials informatics in academia and industry is discussed, the need for educational advances in Materials informatics is highlighted, and the implementation of a materials informatic course into the curriculum to jump-start interested students with the skills required to succeed in materials informingatics projects is discussed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: ORCID
Added: March 11, 2020

2020 journal article

Partially Fluorinated Copolymers as Oxygen Sensitive(19)F MRI Agents

CHEMISTRY-A EUROPEAN JOURNAL, 26(44), 9982–9990.

By: N. Taylor*, S. Chung*, A. Kwansa n, R. Johnson*, A. Teator*, N. Milliken n, K. Koshlap*, Y. Yingling n, Y. Lee*, F. Leibfarth*

author keywords: F-19 MRI; amphiphilic copolymer; fluorinated monomers; oxygen sensing; polyacrylates
MeSH headings : Fluorine / analysis; Fluorine / chemistry; Halogenation; Magnetic Resonance Imaging; Oxygen / analysis; Oxygen / chemistry; Partial Pressure; Polymers / chemistry
TL;DR: High-performance highly fluorinated monomers are reported that provide a platform to realize water-soluble, partially fluorinated copolymers as 19 F MRI agents with the required sensitivity to quantify solution oxygenation at clinically relevant magnetic field strengths. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: July 20, 2020

2020 journal article

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

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(52), 32891–32901.

By: M. Umerani*, P. Pratakshya*, A. Chatterjee*, J. Sanchez*, H. Kim n, G. Ilc*, M. Kovacic*, C. Magnan* ...

author keywords: reflectin; self-assembly; proteins; biomaterials; optical properties
TL;DR: The molecular-level structure of a model reflectin variant is resolved at the molecular level, a straightforward approach to controlling the assembly of this protein is established, and a correlation between its structural characteristics and light-manipulating properties is established. (via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action (Web of Science)
14. Life Below Water (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 25, 2021

2019 journal article

Biochemical and physiological flexibility accompanies reduced cellulose biosynthesis in Brachypodium cesa1S830N

AoB PLANTS, 11(5).

By: C. Brabham*, A. Singh n, J. Stork*, Y. Rong*, I. Kumar*, K. Kikuchi*, Y. Yingling n, T. Brutnell*, J. Rose*, S. Debolt*

Ed(s): P. Jameson

TL;DR: Molecular dynamic simulations of the CELLULOSE SYNTHASE A (CESA) structure with modelled membrane interactions illustrated that Bdcesa1S830N exhibited structural changes in the translated gene product responsible for reduced cellulose biosynthesis. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: December 16, 2019

2019 chapter

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

In E. Maginn & J. Errington (Eds.), Foundations of Molecular Modeling and Simulation: Select Papers from FOMMS 2018 (pp. 75–100).

By: T. Deaton n, F. Aydin*, N. Li n, X. Chu*, M. Dutt* & Y. Yingling n

Ed(s): E. Maginn & J. Errington

Sources: NC State University Libraries, NC State University Libraries
Added: May 3, 2021

2019 journal article

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

ACS Nano, 13(2), 1795–1804.

author keywords: nanoparticle heterogeneity; nanoparticle characterization; surface chemistry heterogeneity; nanoparticle surface functionalization; high-performance liquid chromatography; fluorescence correlation spectroscopy; molecular dynamics
MeSH headings : Chromatography, High Pressure Liquid / methods; Nanomedicine / methods; Nanoparticles / chemistry; Silicon Dioxide / chemistry
TL;DR: Applying a combination of high-performance liquid chromatography and gel permeation chromatography to ultra-small (<10 nm diameter) poly(ethylene glycol)-coated (PEGylated) fluorescent core-shell silica nanoparticles elucidate here previously unknown surface heterogeneities resulting from varying dye conjugation to nanoparticle silica cores and surfaces. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: March 25, 2019

2019 journal article

Intrinsically disordered proteins access a range of hysteretic phase separation behaviors

Science Advances, 5(10), eaax5177.

Contributors: F. Quiroz*, N. Li n, S. Roberts*, P. Weber*, M. Dzuricky*, I. Weitzhandler*, Y. Yingling n, A. Chilkoti*

MeSH headings : Amino Acids / chemistry; Antifreeze Proteins / chemistry; Circular Dichroism; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Intrinsically Disordered Proteins / chemistry; Molecular Dynamics Simulation; Nanoparticles / chemistry; Phase Transition; Proline / chemistry; Temperature; Urea / chemistry
TL;DR: It is discovered that IDP polymers composed of repeat motifs that encode LCST or UCST phase behavior can access a wide spectrum of nonequilibrium, hysteretic phase behaviors and hysteresis is tunable and that it emerges through increasingly stable interchain interactions in the insoluble phase. (via Semantic Scholar)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: November 4, 2019

2019 journal article

Simulations of Cellulose Synthesis Initiation and Termination in Bacteria

The Journal of Physical Chemistry B, 123(17), 3699–3705.

By: H. Yang*, J. McManus*, D. Oehme*, A. Singh n, Y. Yingling n, M. Tien*, J. Kubicki*

Contributors: H. Yang*, J. McManus*, D. Oehme*, A. Singh n, Y. Yingling n, M. Tien*, J. Kubicki*

MeSH headings : Cellulose / biosynthesis; Cellulose / chemistry; Glucosyltransferases / metabolism; Molecular Dynamics Simulation; Particle Size; Quantum Theory; Rhodobacter sphaeroides / enzymology; Surface Properties
TL;DR: It is suggested that cellulose synthesis in bacterial CESA can be initiated with H2O molecules, which opens up the possibility of generating mutants that would produce cellulose chains with desired chain lengths that could have applications in the biofuel and textile fields that depend on the DOP of cellulose Chains. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, ORCID, NC State University Libraries
Added: December 16, 2019

2018 journal article

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

ACS Omega, 3(10), 14027–14038.

By: M. McGoorty n, A. Singh n, T. Deaton n, B. Peterson n, C. Taliaferro n, Y. Yingling n, F. Castellano n

Contributors: M. McGoorty n, A. Singh n, T. Deaton n, B. Peterson n, C. Taliaferro n, Y. Yingling n, F. Castellano n

TL;DR: A combination of nanoscale particle characterization techniques, static and dynamic photoluminescence spectroscopic studies, along with atomistic molecular dynamics simulations of these soft materials suggests the formation of small, heterogeneous nanoaggregate structures, wherein the sulfonated diimine ancillary ligand serves as a pro-aggregating subunit in all instances. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: November 26, 2018

2018 journal article

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

JOURNAL OF INTEGRATIVE PLANT BIOLOGY, 60(6), 481–497.

By: T. Scavuzzo-Duggan*, A. Chaves*, A. Singh n, L. Sethaphong n, E. Slabaugh n, Y. Yingling n, C. Haigler n, A. Roberts*

Contributors: T. Scavuzzo-Duggan*, A. Chaves*, A. Singh n, L. Sethaphong n, E. Slabaugh n, Y. Yingling n, C. Haigler n, A. Roberts*

MeSH headings : Amino Acid Sequence; Bryopsida / enzymology; Cellulose / metabolism; Gene Knockout Techniques; Genetic Complementation Test; Genetic Vectors / metabolism; Glucosyltransferases / chemistry; Glucosyltransferases / classification; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Isoenzymes / chemistry; Isoenzymes / metabolism; Models, Molecular; Phylogeny
TL;DR: Sequence analysis and computational modeling showed that the CSR is intrinsically disordered and contains predicted molecular recognition features, consistent with a possible role in CESA oligomerization and explaining the evolution of class-specific sequences without selection for class- specific function. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2018 journal article

Design of Histone-Mimic Nanoparticles for DNA and RNA Compaction using Molecular Modeling

Biophysical Journal, 114(3), 362a.

By: M. Manning n, J. Nash n & Y. Yingling n

Sources: Crossref, NC State University Libraries
Added: January 19, 2020

2018 journal article

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

Biomacromolecules, 19(8), 3525–3535.

By: R. Gu*, T. Oweida n, Y. Yingling n, A. Chilkoti* & S. Zauscher*

Contributors: R. Gu*, T. Oweida n, Y. Yingling n, A. Chilkoti* & S. Zauscher*

MeSH headings : Biocatalysis; DNA Nucleotidylexotransferase / metabolism; DNA, Single-Stranded / chemical synthesis; DNA, Single-Stranded / chemistry; Deoxyribonucleases / metabolism; Hydrolysis; Protein Binding; Purine Nucleosides / chemistry
TL;DR: It is discovered that increasing the size and density of unnatural nucleobases enhances ssDNA resistance to degradation in the presence of exonuclease I, DNase I, and human serum, and this suggests that incorporating nucleobase-modified nucleotides into ssDNA, using enzymatic polymerization, is an easy and efficient strategy to prolong and tune the half-life of DNA-based materials in nucleases-containing environments. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, ORCID, NC State University Libraries
Added: December 16, 2019

2018 journal article

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

Biointerphases, 13(6), 06D502.

By: M. Manning n, A. Kwansa n, T. Oweida n, J. Peerless n, A. Singh n & Y. Yingling n

Contributors: M. Manning n, A. Kwansa n, T. Oweida n, J. Peerless n, A. Singh n & Y. Yingling n

MeSH headings : Drug Carriers / chemistry; Humans; Nanomedicine / economics; Nanomedicine / methods; Nanomedicine / trends; Nanoparticles / chemistry; Surface Properties; Technology, Pharmaceutical / economics; Technology, Pharmaceutical / methods; Technology, Pharmaceutical / trends
TL;DR: A comprehensive understanding of ligand design principles lies in the cost associated with synthesizing and characterizing diverse ligand chemistries and the ability to carefully assess the structural integrity of biomolecules upon interactions with nanoparticles. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: December 3, 2018

2018 journal article

Sequence Directionality Dramatically Affects LCST Behavior of Elastin-Like Polypeptides

Biomacromolecules, 19(7), 2496–2505.

By: N. Li n, S. Roberts*, F. Quiroz*, A. Chilkoti* & Y. Yingling n

Contributors: N. Li n, S. Roberts*, F. Quiroz*, A. Chilkoti* & Y. Yingling n

MeSH headings : Amino Acid Motifs; Elastin / chemistry; Molecular Dynamics Simulation; Phase Transition; Protein Domains; Temperature
TL;DR: The results from MD simulations indicated that a change in sequence order results in significant differences in the dynamics of the specific residues, especially valines, which lead to extensive changes in the conformations of VPGVG and VGPVG pentamers and, consequently, dissimilar propensities for secondary structure formation and overall structure of polypeptides. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: August 6, 2018

2018 journal article

Soft Matter Informatics: Current Progress and Challenges

Advanced Theory and Simulations, 2(1), 1800129.

By: J. Peerless, N. Milliken, T. Oweida, M. Manning & Y. Yingling*

Contributors: J. Peerless, N. Milliken, T. Oweida, M. Manning & Y. Yingling*

author keywords: databases; informatics; machine learning; polymers; soft matter
TL;DR: The current ability to extract and analyze the information from the PoLyInfo database is demonstrated by the fitting of the Flory–Fox equation for glass transition temperature for several polymers. (via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: December 16, 2019

2018 journal article

Wrapping Nanocellulose Nets around Graphene Oxide Sheets

Angewandte Chemie International Edition, 57(28), 8508–8513.

By: R. Xiong*, H. Kim n, L. Zhang*, V. Korolovych*, S. Zhang*, Y. Yingling n, V. Tsukruk*

Contributors: R. Xiong*, H. Kim n, L. Zhang*, V. Korolovych*, S. Zhang*, Y. Yingling n, V. Tsukruk*

author keywords: cellulose nanofibers; graphene; mechanical properties; self-assembly; water transport
TL;DR: An efficient and universal amphiphilicity-driven assembly strategy to construct "hairy" flexible hybrid nanosheets with a 1D cellulose nanofibers net conformally wrapped around 2D graphene oxide (GO) monolayers, allowing fast water transport combined with high filtration efficiency. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: August 6, 2018

2017 review

Advances in Molecular Modeling of Nanoparticle Nucleic Acid Interfaces

[Review of ]. BIOCONJUGATE CHEMISTRY, 28(1), 3–10.

By: J. Nash n, A. Kwansa n, J. Peerless n, H. Kim n & Y. Yingling n

Contributors: J. Nash n, A. Kwansa n, J. Peerless n, H. Kim n & Y. Yingling n

MeSH headings : Ligands; Models, Molecular; Nanoparticles / chemistry; Nucleic Acids / chemistry; Solvents / chemistry
TL;DR: This Topical Review briefly review computational methods relevant to the interactions of inorganic NPs and nucleic acids and highlight recent insights obtained from various computational methods that were applied to studies of in organic nanoparticle-nanoparticle and nanoparticles-nucleic acid interfaces. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2017 journal article

Effect of C 60 adducts on the dynamic structure of aromatic solvation shells

Chemical Physics Letters, 678, 79–84.

By: J. Peerless n, G. Bowers n, A. Kwansa n & Y. Yingling n

Contributors: J. Peerless n, G. Bowers n, A. Kwansa n & Y. Yingling n

author keywords: Fullerenes; Solubility; Molecular dynamics simulations; Structure analysis
UN Sustainable Development Goal Categories
Sources: Crossref, ORCID, NC State University Libraries
Added: December 16, 2019

2017 journal article

Effect of Graphene Oxidation Rate on Adsorption of Poly-Thymine Single Stranded DNA

Advanced Materials Interfaces, 4(8), 1601168.

By: H. Kim n, B. Farmer n & Y. Yingling n

Contributors: Y. Yingling n, B. Farmer n & H. Kim n

UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Crossref, ORCID, NC State University Libraries, NC State University Libraries
Added: August 6, 2018

2017 journal article

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

Biomacromolecules, 19(2), 298–306.

By: L. Li*, N. Li n, Q. Tu*, O. Im*, C. Mo*, W. Han*, W. Fuss n, N. Carroll* ...

Contributors: L. Li*, N. Li n, Q. Tu*, O. Im*, C. Mo*, W. Han*, W. Fuss n, N. Carroll* ...

MeSH headings : Adsorption; Elastin / chemistry; Micelles; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Protein Precursors / chemistry; Silicon Dioxide / chemistry; Wettability
TL;DR: It is demonstrated that genetic incorporation of a silica-binding peptide results in enhanced adsorption of these block copolymers onto silica surfaces as measured by quartz crystal microbalance and ellipsometry, and wettability measurements suggest that surface immobilization hampers the temperature-dependent conformational change of ELP micelles, while adsorbed ELP unimers retain their thermally responsive property at interfaces. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, Crossref, NC State University Libraries
Added: August 6, 2018

2017 journal article

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

ACS Applied Materials & Interfaces, 9(11), 10203–10213.

By: Q. Tu*, H. Kim n, T. Oweida n, Z. Parlak*, Y. Yingling n & S. Zauscher*

Contributors: Q. Tu*, H. Kim n, T. Oweida n, Z. Parlak*, Y. Yingling n & S. Zauscher*

author keywords: graphene; self-assembled monolayer; contact resonance AFM; out-of-plane Young's modulus; molecular dynamics simulation; interfacial water
TL;DR: It is shown that the head group chemistry of a SAM, which affects the interfacial interactions, can have a significant effect on the out-of-plane elastic modulus of the graphene-SAM heterostructure. (via Semantic Scholar)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: August 6, 2018

2017 journal article

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

Journal of Materials Science, 53(8), 5766–5776.

By: H. Kim n, T. Oweida n & Y. Yingling n

Contributors: Y. Yingling n, T. Oweida n & H. Kim n

Sources: Web Of Science, ORCID, Crossref, NC State University Libraries
Added: August 6, 2018

2017 journal article

Macromol. Rapid Commun. 20/2017

Macromolecular Rapid Communications, 38(20).

By: N. Li n, H. Kuang*, W. Fuss n, S. Zauscher*, E. Kokkoli* & Y. Yingling n

Source: ORCID
Added: January 6, 2020

2017 journal article

Physisorption: Effect of Graphene Oxidation Rate on Adsorption of Poly-Thymine Single Stranded DNA (Adv. Mater. Interfaces 8/2017)

Advanced Materials Interfaces, 4(8).

By: H. Kim n, B. Farmer n & Y. Yingling n

UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2017 journal article

Salt Responsive Morphologies of ssDNA-Based Triblock Polyelectrolytes in Semi-Dilute Regime: Effect of Volume Fractions and Polyelectrolyte Length

Macromolecular Rapid Communications, 38(20), 1700422.

By: N. Li n, H. Kuang*, W. Fuss n, S. Zauscher*, E. Kokkoli* & Y. Yingling n

Contributors: N. Li n, H. Kuang*, W. Fuss n, S. Zauscher*, E. Kokkoli* & Y. Yingling n

author keywords: block copolymers; dissipative particle dynamics simulations; polyelectrolytes; responsive morphology; self-assembly; ssDNA
MeSH headings : Cryoelectron Microscopy; DNA, Single-Stranded / chemistry; Hydrophobic and Hydrophilic Interactions; Micelles; Osmolar Concentration; Polyelectrolytes / chemistry; Sodium Chloride / chemistry; Solvents / chemistry
TL;DR: Insight is provided into the network morphology and its changes by calculating the aggregation number, number of hydrophobic cores, and percentage of bridge chains in the network by utilizing an implicit solvent ionic strength method for dissipative particle dynamics simulations. (via Semantic Scholar)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: August 6, 2018

2017 journal article

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

ACS Nano, 11(12), 12008–12019.

By: R. Xiong*, H. Kim n, S. Zhang*, S. Kim*, V. Korolovych*, R. Ma*, Y. Yingling n, C. Lu*, V. Tsukruk*

Contributors: R. Xiong*, H. Kim n, S. Zhang*, S. Kim*, V. Korolovych*, R. Ma*, Y. Yingling n, C. Lu*, V. Tsukruk*

author keywords: silk fibroin; cellulose nanofiber; ultrathin membrane; flexible nanocomposites; ultrafast permeation
TL;DR: A spontaneous formation of peculiar "shish kebab" nanostructures with the periodic arrangement of silk fibroin domains along straight segments of cellulose nanofibers is reported, enabling the ultrathin membrane to possess open, transparent, mechanically robust interlocked networks with high mechanical performance. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

A Barley Efflux Transporter Operates in a Na+-Dependent Manner, as Revealed by a Multidisciplinary Platform

Plant Cell, 28(1), 202–218.

By: Y. Nagarajan*, J. Rongala*, S. Luang*, A. Singh n, N. Shadiac*, J. Hayes*, T. Sutton*, M. Gilliham* ...

Contributors: Y. Nagarajan*, J. Rongala*, S. Luang*, A. Singh n, N. Shadiac*, J. Hayes*, T. Sutton*, M. Gilliham* ...

MeSH headings : Anions / metabolism; Binding Sites; Borates / metabolism; Cell-Free System; Computer Simulation; Hordeum / metabolism; Lipid Bilayers / metabolism; Liposomes / metabolism; Membrane Transport Proteins / chemistry; Membrane Transport Proteins / metabolism; Models, Molecular; Permeability; Pichia / metabolism; Plant Proteins / chemistry; Plant Proteins / metabolism; Protein Folding; Protein Multimerization; Sodium / metabolism; Triticum / metabolism
TL;DR: Using alanine scanning, molecular dynamics simulations, and transport measurements, it is shown that conductance by Bot1 is abolished by removal of the Na+ ion binding site, which enhances the understanding of the permeation functions of Bot1. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

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

BIOINTERPHASES, 11(4).

By: J. Nash n, T. Tucker n, W. Therriault n & Y. Yingling n

Contributors: Y. Yingling n, W. Therriault n, T. Tucker n & J. Nash n

MeSH headings : Cations / metabolism; Gold / metabolism; Molecular Dynamics Simulation; Nanoparticles / chemistry; Nanoparticles / metabolism; Nucleic Acids / metabolism
TL;DR: Overall, the results show that control over ssNA structure may be achieved with cationic NPs with a charge of more than 30, but the extent of the structural changes depends on sequence. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

Bionanocomposites: Silk Fibroin-Substrate Interactions at Heterogeneous Nanocomposite Interfaces (Adv. Funct. Mater. 35/2016)

Advanced Functional Materials, 26(35), 6496–6496.

By: A. Grant*, H. Kim n, T. Dupnock n, K. Hu*, Y. Yingling n & V. Tsukruk*

Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2016 journal article

Comparative Structural and Computational Analysis Supports Eighteen Cellulose Synthases in the Plant Cellulose Synthesis Complex

Scientific Reports, 6(1).

By: B. Nixon*, K. Mansouri n, A. Singh n, J. Du*, J. Davis n, J. Lee n, E. Slabaugh n, V. Vandavasi* ...

Contributors: B. Nixon*, K. Mansouri n, A. Singh n, J. Du*, J. Davis n, J. Lee n, E. Slabaugh n, V. Vandavasi* ...

MeSH headings : Cellulose / biosynthesis; Cellulose / chemistry; Glucosyltransferases / chemistry; Models, Molecular; Plant Proteins / chemistry; Protein Domains; Protein Folding; Protein Structure, Quaternary
TL;DR: Improved transmission electron microscopy images and image averages of the rosette-type CSC are obtained, revealing the frequent triangularity and average cross-sectional area in the plasma membrane of its individual lobes and multifaceted data support a rosettes CSC with 18 CESAs that mediates the synthesis of a fundamental microfibril composed of 18 glucan chains. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2016 journal article

Design of Potent and Controllable Anticoagulants Using DNA Aptamers and Nanostructures

MOLECULES, 21(2).

By: A. Rangnekar n, J. Nash n, B. Goodfred n, Y. Yingling n & T. LaBean n

Contributors: A. Rangnekar n, J. Nash n, B. Goodfred n, Y. Yingling n & T. LaBean n

author keywords: thrombin; DNA aptamers; anticoagulation; DNA nanotechnology
MeSH headings : Anticoagulants / chemistry; Anticoagulants / pharmacology; Aptamers, Nucleotide / chemistry; Aptamers, Nucleotide / pharmacology; Drug Design; Drug Evaluation, Preclinical; Humans; Molecular Dynamics Simulation; Nanostructures / chemistry; Partial Thromboplastin Time
TL;DR: By using DNA strand displacement, this work was able to turn the coagulation cascade off and on as desired, thereby enabling significantly better control over blood coagulating. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

Emulsion-Based RIR-MAPLE Deposition of Conjugated Polymers: Primary Solvent Effect and Its Implications on Organic Solar Cell Performance

ACS APPLIED MATERIALS & INTERFACES, 8(30), 19494–19506.

By: W. Ge*, N. Li n, R. McCormick*, E. Lichtenberg*, Y. Yingling n & A. Stiff-Roberts

Contributors: A. Stiff-Roberts, Y. Yingling n, E. Lichtenberg*, R. McCormick*, N. Li n & W. Ge*

author keywords: MAPLE; emulsion target; polymer films; organic solar cells; dissipative particle dynamics
TL;DR: The mechanism of polymer film formation using emulsion-based RIR-MAPLE is unveiled and insight and direction is provided to determine the best ways to take advantage of the emulsion target approach to control film properties for different applications. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

Fluorescence Blinking as an Output Signal for Biosensing

ACS Sensors, 1(11), 1295–1300.

By: B. Roark*, J. Tan*, A. Ivanina*, M. Chandler*, J. Castaneda*, H. Kim n, S. Jawahar*, M. Viard* ...

Contributors: K. Afonin*, M. Jones*, Y. Yingling n, K. Wustholz*, S. Talic*, M. Viard*, S. Jawahar*, H. Kim n ...

author keywords: fluorescence blinking; quantum dots; lattices; biosensors; K-ras; nucleic acid engineering; strand displacement
TL;DR: This work demonstrates the first biosensing strategy that relies on quantum dot (QD) fluorescence blinking to report the presence of a target molecule, and does not require the analyte to induce any fluorescence intensity or color changes, making it readily applicable to a wide range of target species. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

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

BIOMACROMOLECULES, 17(1), 111–118.

By: B. Zhao n, N. Li n, Y. Yingling n & C. Hall n

Contributors: C. Hall n, Y. Yingling n, N. Li n & B. Zhao n

MeSH headings : Cold Temperature; Elastin / chemistry; Hydrogen Bonding; Oligopeptides / chemistry; Peptides / chemistry; Pharmaceutical Solutions / chemistry; Transition Temperature; Water / chemistry
TL;DR: Simulation of the physical origin of the lower critical solution temperature (LCST) behavior of elastin-like polypeptides (ELPs) finds evidence for properties changes associated with LCST behavior in a single molecule by performing long atomic-level molecular dynamics simulation on the ELP sequences for four different length peptides over a wide range of temperatures. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2016 article

Molecular Dynamics Simulations of Nano-biomaterials

Encyclopedia of Nanotechnology, pp. 2260–2269.

By: M. Pasquinelli n & Y. Yingling n

Source: ORCID
Added: December 6, 2018

2016 journal article

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

Cellulose, 23(1), 145–161.

By: L. Sethaphong n, J. Davis n, E. Slabaugh n, A. Singh n, C. Haigler n & Y. Yingling n

Contributors: Y. Yingling n, C. Haigler n, A. Singh n, E. Slabaugh n, J. Davis n & L. Sethaphong n

author keywords: Arabidopsis thaliana; Cellulose synthesis; Computational protein structure prediction; Isoform specificity; Mutant complementation
TL;DR: Modeling of the mutant P-CR of Atcesa8R362K (fra6) suggested that changes in local structural stability and surface electrostatics may cause the mutant phenotype, and results provide structural clues about the function of plant-specific regions of CESA. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2016 journal article

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

MRS Advances, 1(25), 1883–1889.

By: H. Kim n, S. Huang n & Y. Yingling n

Contributors: Y. Yingling n, S. Huang n & H. Kim n

UN Sustainable Development Goal Categories
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

Silk Fibroin-Substrate Interactions at Heterogeneous Nanocomposite Interfaces

ADVANCED FUNCTIONAL MATERIALS, 26(35), 6380–6392.

By: A. Grant*, H. Kim n, T. Dupnock n, K. Hu*, Y. Yingling n & V. Tsukruk*

Contributors: A. Grant*, H. Kim n, T. Dupnock n, K. Hu*, Y. Yingling n & V. Tsukruk*

UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

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(32), 22062–22069.

By: H. Kim n, D. Eom*, Y. Koo* & Y. Yingling n

Contributors: Y. Yingling n, Y. Koo*, D. Eom* & H. Kim n

MeSH headings : Candida / enzymology; Catalysis; Cations; Fungal Proteins / metabolism; Hydrophobic and Hydrophilic Interactions; Lipase / metabolism; Molecular Dynamics Simulation
TL;DR: Overall, this study indicates that a high ion coordination number or the presence of a long hydrophobic tail can facilitate ion-protein interactions that cause structural distortions and a decrease in CALB enzyme activity in ILs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: August 6, 2018

2016 journal article

When in silico meets in vitro: Molecular basis of function of an anion-permeable efflux transporter from barley (Hordeum vulgare L.)

Abstracts of Papers of the American Chemical Society. https://publons.com/wos-op/publon/382040/

Contributors: A. Singh, Y. Nagarajan, M. Hrmova & Y. Yingling

Source: ORCID
Added: January 6, 2020

2015 journal article

An Implicit Solvent Ionic Strength (ISIS) Method to Model Polyelectrolyte Systems with Dissipative Particle Dynamics

MACROMOLECULAR THEORY AND SIMULATIONS, 24(1), 7–12.

By: N. Li n, W. Fuss n & Y. Yingling n

Contributors: Y. Yingling n, W. Fuss n & N. Li n

author keywords: block copolymer; dissipative particle dynamics; polyelectrolyte; solvent ionic strength; self-assembly
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2015 journal article

CELLULOSE SYNTHASE INTERACTIVE1 Is Required for Fast Recycling of Cellulose Synthase Complexes to the Plasma Membrane in Arabidopsis

The Plant Cell, 27(10), tpc.15.00442.

By: L. Lei*, A. Singh n, L. Bashline*, S. Li*, Y. Yingling n & Y. Gu*

Contributors: L. Lei*, A. Singh n, L. Bashline*, S. Li*, Y. Yingling n & Y. Gu*

MeSH headings : Arabidopsis / genetics; Arabidopsis / physiology; Arabidopsis / ultrastructure; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Carrier Proteins / genetics; Carrier Proteins / metabolism; Cell Membrane / enzymology; Cellulose / metabolism; Clathrin / metabolism; Endocytosis; Genes, Reporter; Glucosyltransferases / genetics; Glucosyltransferases / metabolism; Microtubules / metabolism; Models, Molecular; Protein Transport; Seedlings / genetics; Seedlings / physiology; Seedlings / ultrastructure
TL;DR: This study establishes a model in which CSI1-dependent SmaCCs/MASCs are formed through a process that involves endocytosis, which represents an important mechanism for plants to quickly regulate cellulose synthesis under abiotic stress. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2015 journal article

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics

ACS NANO, 9(12), 12374–12382.

By: J. Nash n, A. Singh n, N. Li n & Y. Yingling n

Contributors: Y. Yingling n, N. Li n, A. Singh n & J. Nash n

author keywords: gold nanoparticles; DNA compaction; RNA compaction; molecular dynamics simulations; nanoparticle binding; nucleosome
MeSH headings : Gold / chemistry; Histones / chemistry; Metal Nanoparticles / chemistry; Molecular Dynamics Simulation; Nucleic Acids / chemistry; Nucleic Acids / metabolism; Nucleic Acids / ultrastructure
TL;DR: Large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2015 journal article

Cover Picture: Macromol. Theory Simul. 1∕2015

Macromolecular Theory and Simulations, 24(1), 1–1.

By: N. Li n, W. Fuss n & Y. Yingling n

Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2015 journal article

Effect of NP shape and ligand flexibility in the design of nucleic acid wrapping NPs

Abstracts of Papers of the American Chemical Society. https://publons.com/wos-op/publon/28057470/

Contributors: J. Nash, A. Singh, N. Li & Y. Yingling

Source: ORCID
Added: January 6, 2020

2015 journal article

Effect of surface polarity on physisorption of biomolecules: Molecular modeling

Abstracts of Papers of the American Chemical Society. https://publons.com/publon/28057471/

Contributors: Y. Yingling & H. Kim

Source: ORCID
Added: January 6, 2020

2015 journal article

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

JOURNAL OF PHYSICAL CHEMISTRY B, 119(49), 15344–15352.

By: J. Peerless n, G. Bowers n, A. Kwansa n & Y. Yingling n

Contributors: Y. Yingling n, A. Kwansa n, G. Bowers n & J. Peerless n

TL;DR: The determined dependence of the solvation-shell structure on the geometric shape of the solvent might allow for enhanced control of fullerene solution-phase behavior during processing by chemically tailoring the solvent molecular structure, potentially diminishing the need for costly and environmentally harmful halogenated solvents and/or additives. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2015 journal article

Gold nanoparticle-nucleic acid modeling using GPU-accelerated molecular dynamics

Abstracts of Papers of the American Chemical Society. https://publons.com/publon/28057466/

Contributors: Y. Yingling, A. Kwansa & J. Nash

Source: ORCID
Added: January 6, 2020

2015 journal article

How Cellulose Elongates-A QM/MM Study of the Molecular Mechanism of Cellulose Polymerization in Bacterial CESA

JOURNAL OF PHYSICAL CHEMISTRY B, 119(22), 6525–6535.

By: H. Yang*, J. Zimmer*, Y. Yingling n & J. Kubicki*

Contributors: J. Kubicki*, Y. Yingling n, J. Zimmer* & H. Yang*

MeSH headings : Biocatalysis; Carbohydrate Conformation; Cellulose / chemistry; Cellulose / metabolism; Enzyme Activation; Glucose / chemistry; Glucose / metabolism; Glucosyltransferases / chemistry; Glucosyltransferases / metabolism; Glycosylation; Molecular Dynamics Simulation; Polymerization; Protein Conformation; Protons; Quantum Theory; Rhodobacter / enzymology; Uridine Diphosphate / chemistry; Uridine Diphosphate / metabolism; Water / chemistry
TL;DR: This study provides detailed insights into how cellulose is extended by one glucose molecule at a time and how the individual glucose units align into cellobiose repeating units. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2015 review

Microtubules and cellulose biosynthesis: the emergence of new players

[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 28, 76–82.

By: S. Li*, L. Lei*, Y. Yingling n & Y. Gu*

Contributors: S. Li*, L. Lei*, Y. Yingling n & Y. Gu*

MeSH headings : Cell Membrane / metabolism; Cellulose / biosynthesis; Glucosyltransferases / genetics; Glucosyltransferases / metabolism; Microfibrils / metabolism; Microtubules / metabolism; Plant Physiological Phenomena; Plant Proteins / genetics; Plant Proteins / metabolism
TL;DR: Characterization of CSIs and additional cellulose synthase-associated proteins will greatly advance the knowledge of how cellulose microfibrils are organized. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2015 journal article

Molecular description of LCST behavior of elastin-like peptides poly(VPGVG) and poly(VGPVG)

Abstracts of Papers of the American Chemical Society. https://publons.com/publon/28057468/

Contributors: Y. Yingling & N. Li

Source: ORCID
Added: January 6, 2020

2015 journal article

Morphological and rheological properties of aqueous micellar network of polyelectrolyte block copolymers

Abstracts of Papers of the American Chemical Society. https://publons.com/publon/28057469/

Contributors: Y. Yingling, W. Fuss & N. Li

Source: ORCID
Added: January 6, 2020

2015 journal article

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

SOFT MATTER, 11(42), 8236–8245.

By: N. Li n, W. Fuss n, L. Tang*, R. Gu*, A. Chilkoti*, S. Zauscher*, Y. Yingling n

Contributors: N. Li n, W. Fuss n, L. Tang*, R. Gu*, A. Chilkoti*, S. Zauscher*, Y. Yingling n

MeSH headings : Computer Simulation; DNA, Single-Stranded / chemistry; Electrolytes / chemistry; Micelles; Models, Chemical; Polymers / chemistry; Solvents / chemistry
TL;DR: Overall, this work was able to predict the salt-responsive morphology of polyelectrolyte materials in aqueous solution and show that a spherical-cylindrical-lamellar change in morphology can be obtained through an increase in solvent ionic strength or a decrease of poly Electrolyte length. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2015 journal article

Simulations of the self-assembly of polyelectrolyte block copolymers using dissipative particle dynamics with an implicit solvent ionic strength (ISIS) method

Abstracts of Papers of the American Chemical Society. https://publons.com/publon/28057467/

Contributors: Y. Yingling, W. Fuss & N. Li

Source: ORCID
Added: January 6, 2020

2014 journal article

Cellulose synthases: new insights from crystallography and modeling

Trends in Plant Science, 19(2), 99–106.

By: E. Slabaugh n, J. Davis n, C. Haigler n, Y. Yingling n & J. Zimmer*

Contributors: J. Zimmer*, Y. Yingling n, C. Haigler n, J. Davis n & E. Slabaugh n

MeSH headings : Catalytic Domain; Crystallography; Glucosyltransferases / chemistry; Models, Molecular; Plant Proteins / chemistry
TL;DR: It is shown how the structures of CelS proteins can be used to generate hypotheses for experiments testing mechanisms of glucan synthesis and translocation in plant CelS, and how these structures impact the understanding of the synthesis of cellulose and other extracellular polysaccharides. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2014 journal article

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

Journal of Experimental Botany, 65(22), 6645–6653.

Contributors: E. Slabaugh n, L. Sethaphong n, C. Xiao*, J. Amick n, C. Anderson*, C. Haigler n, Y. Yingling n

author keywords: Cellulose biosynthesis; CESA; genetic complementation; protein structural modelling; rsw1 mutant; transmembrane helix
MeSH headings : Amino Acid Sequence; Arabidopsis / enzymology; Arabidopsis / genetics; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Biocatalysis; Computational Biology; Glucosyltransferases / chemistry; Glucosyltransferases / genetics; Glucosyltransferases / metabolism; Molecular Sequence Data; Mutant Proteins / metabolism; Mutation; Phenotype; Protein Structure, Secondary; Recombinant Fusion Proteins / metabolism; Sequence Alignment; Structure-Activity Relationship
TL;DR: Computational modelling of peptide structure, genetic complementation in Arabidopsis thaliana, and confocal microscopy provide evidence that a region between two transmembrane helices may adopt two predominant structural conformations that affect the function of plant cellulose synthase. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2014 journal article

Enzymatic Polymerization of High Molecular Weight DNA Amphiphiles That Self-Assemble into Star-Like Micelles

ADVANCED MATERIALS, 26(19), 3050–3054.

By: L. Tang*, V. Tjong*, N. Li n, Y. Yingling n, A. Chilkoti* & S. Zauscher*

Contributors: L. Tang*, V. Tjong*, N. Li n, Y. Yingling n, A. Chilkoti* & S. Zauscher*

author keywords: polynucleotides; polymerase; self-assembly; AFM; dissipative particle dynamics
MeSH headings : Biocatalysis; Boron Compounds / chemistry; DNA, Single-Stranded / chemistry; DNA, Single-Stranded / metabolism; Enzymes / metabolism; Exodeoxyribonucleases / metabolism; Micelles; Microscopy, Atomic Force; Nanostructures / chemistry; Polymerization; Polynucleotides / chemistry
TL;DR: High molecular weight ssDNA amphiphiles synthesized by enzymatic polymerization self-assemble into "hairy", star-like micelles, shown in the AFM image and the DPD snapshot. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2014 journal article

Molecular Description of the LCST Behavior of an Elastin-Like Polypeptide

BIOMACROMOLECULES, 15(10), 3522–3530.

By: N. Li n, F. Quiroz*, C. Hall*, A. Chilkoti* & Y. Yingling*

Contributors: N. Li n, F. Quiroz*, C. Hall*, A. Chilkoti* & Y. Yingling*

MeSH headings : Cold Temperature; Elastin / chemistry; Hydrophobic and Hydrophilic Interactions; Oligopeptides / chemistry; Peptides / chemistry; Protein Structure, Secondary; Solutions / chemistry; Solvents / chemistry; Transition Temperature; Water / chemistry
TL;DR: The results lead to propose that the LCST phase behavior of poly(VPGVG)18 is a collective phenomenon that originates from the correlated gradual changes in single polypeptide structure and the abrupt change in properties of hydration water around the peptide and is a result of a competition between peptide- peptide and peptides-water interactions. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2014 journal article

Persistence Length of Single Stranded DNA: Effect of Length, Sequence and Surface

Biophysical Journal.

Contributors: Y. Yingling n & H. Kim n

TL;DR: This research provided atomistic understanding of dynamics and conformational changes of single stranded DNA under various conditions; the length and sequence dependence as well as the effect of surface immobilization. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2014 journal article

Progress in molecular modelling of DNA materials

MOLECULAR SIMULATION, 40(10-11), 777–783.

By: N. Li n, H. Kim n, J. Nash n, M. Lim n & Y. Yingling n

Contributors: Y. Yingling n, M. Lim n, J. Nash n, H. Kim n & N. Li n

author keywords: molecular modelling; DNA materials; computer simulations
TL;DR: The recent advances in atomistic and coarse-grained force fields along with simulations of DNA-based materials, as applied to DNA–nanoparticle assemblies for controlled material morphology, DNA–surface interactions for biosensor development and DNA origami are reviewed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2014 journal article

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

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16(7), 2944–2953.

By: H. Kim n, S. Ha*, L. Sethaphong n, Y. Koo* & Y. Yingling n

Contributors: H. Kim n, S. Ha*, L. Sethaphong n, Y. Koo* & Y. Yingling n

MeSH headings : 1-Butanol / chemistry; Esterification; Fungal Proteins / chemistry; Fungal Proteins / metabolism; Ionic Liquids / chemistry; Lipase / chemistry; Lipase / metabolism; Molecular Dynamics Simulation; Protein Conformation; Solvents / chemistry; Vinyl Compounds / chemistry; Water / chemistry; tert-Butyl Alcohol / chemistry
TL;DR: The results demonstrate that the conformational changes of the active site cavity are directly related to enzyme activity and decrease and the electrostatic energy between solvents in this study and CALB is correlated with the structural changes leading to differences in enzyme activity. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2013 journal article

Correlating fullerene diffusion with the polythiophene morphology: molecular dynamics simulations

SOFT MATTER, 9(42), 10048–10055.

By: R. Pani n, B. Bond n, G. Krishnan n & Y. Yingling n

Contributors: Y. Yingling n, G. Krishnan n, B. Bond n & R. Pani n

UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2013 journal article

Modeling polymer/biopolymer and nanoparticle interactions: Prediction of materials morphology

Abstracts of Papers of the American Chemical Society. https://publons.com/publon/28057478/

Contributors: Y. Yingling

Source: ORCID
Added: January 6, 2020

2013 journal article

Tertiary model of a plant cellulose synthase

Proceedings of the National Academy of Sciences, 110(18), 7512–7517.

By: L. Sethaphong*, C. Haigler n, J. Kubicki*, J. Zimmer*, D. Bonetta*, S. DeBolt*, Y. Yingling*

Contributors: Y. Yingling*, S. DeBolt*, D. Bonetta*, J. Zimmer*, J. Kubicki*, C. Haigler n, L. Sethaphong*

author keywords: rosette cellulose synthase complex; molecular modeling; protein structure prediction; GlycosylTransferase Family 2; beta-1,4-glucan polymerization
MeSH headings : Arabidopsis / enzymology; Bacteria / enzymology; Computational Biology; Cytosol / enzymology; Glucosyltransferases / chemistry; Glucosyltransferases / genetics; Gossypium / enzymology; Models, Molecular; Mutation / genetics; Phenotype; Protein Structure, Quaternary; Protein Structure, Secondary; Protein Structure, Tertiary
TL;DR: The predicted tertiary structure of cotton CESA provides a platform for the biochemical engineering of plant CESAs and supports the importance of the plant-conserved region and/or class-specific region in CESA oligomerization to form the multimeric cellulose–synthesis complexes that are characteristic of plants. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2013 journal article

Tuning DNA Bending with Charged Nanoparticles: Molecular Simulations

Biophysical Journal, 104(2), 29a.

By: A. Singh n, N. Li n & Y. Yingling n

Contributors: A. Singh n, N. Li n & Y. Yingling n

TL;DR: By tuning the ligand chemistry and its density of GNP the authors can control the binding modes and the structural mechanics of DNA. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2013 conference paper

X3DBio2: A visual analysis tool for biomolecular structure comparison

In P. C. Wong, D. L. Kao, M. C. Hao, C. Chen, & C. G. Healey (Eds.), Visualization and Data Analysis 2013 (Vol. 8654).

By: H. Yi*, S. Thakur*, L. Sethaphong n & Y. Yingling n

Ed(s): P. Wong, D. Kao, M. Hao, C. Chen & C. Healey

Event: IS&T/SPIE Electronic Imaging

author keywords: Molecular structure comparison; Molecular visualization; Interactive exploration; Protein and nucleic acids; Sequence alignment; Structure superposition; Quaternion map; Contact map; Ramachandran plot
TL;DR: A new visual analysis tool, X3DBio2, for 3D biomolecular structure comparison and analysis, designed for elucidation of structural effects of mutations in proteins and nucleic acids and for assessment of time dependent trajectories from molecular dynamics simulations. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018

2012 journal article

Effect of solvent on the interfacial properties between functionalized nanoparticles and polymers

Abstracts of Papers of the American Chemical Society. https://publons.com/wos-op/publon/28057488/

Contributors: R. Pani & Y. Yingling

Source: ORCID
Added: January 6, 2020

2012 journal article

Effect of surface immobilization on the DNA structure and its mechanical properties

Abstracts of Papers of the American Chemical Society. https://publons.com/wos-op/publon/28057502/

Contributors: A. Singh, H. Eksiri & Y. Yingling

Source: ORCID
Added: January 6, 2020

2012 journal article

Gold Nanoparticles: Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation (Adv. Mater. 31/2012)

Advanced Materials, 24(31), 4221–4221.

By: J. Railsback n, A. Singh n, R. Pearce n, T. McKnight*, R. Collazo n, Z. Sitar n, Y. Yingling n, A. Melechko n

Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2012 journal article

Interactions of Gold Nanoparticles with DNA: Interplay of Sequence, Ligands Charge and Polarity

Biophysical Journal.

Contributors: A. Singh n, N. Li n & Y. Yingling n

TL;DR: By tuning the cationic charge density and polarity of GNP the authors can control the binding modes and DNA structural modifications, and observe the distortions of the DNA helical structure strongly depends on the ligand charge density. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2012 chapter

Molecular dynamics simulations of nano-bio materials

In B. Bhushan (Ed.), Encyclopedia of Nanotechnology (pp. 1454–1463).

By: M. Pasquinelli n & Y. Yingling n

Ed(s): B. Bhushan

TL;DR: It is expected that molecular computing will be one of the important technologies, together with other technologies such as synthetic biology, in the age of biomolecular nanotechnology. (via Semantic Scholar)
Sources: NC State University Libraries, NC State University Libraries
Added: January 14, 2021

2012 journal article

Role of Solvent and Dendritic Architecture on the Redox Core Encapsulation

JOURNAL OF PHYSICAL CHEMISTRY A, 116(28), 7593–7599.

By: R. Pani n & Y. Yingling n

Contributors: R. Pani n & Y. Yingling n

TL;DR: The results suggest that peripheral alkyl chains in dendrimers cause steric hindrance, which prevents branches from back folding in chloroform solvent, but in water it reverses the trend, and the presence of a hydrophobic interior and hydrophilic periphery in a dendedrimer improves core encapsulation in water while hindering encapsulations in chlorOform. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2012 journal article

Structure Prediction of a Cellulose Synthase Protein and the Effect of Mutations

Biophysical Journal.

Contributors: A. Singh n, L. Sethaphong n & Y. Yingling n

TL;DR: The predicted structure of CesA explains well the effect of point mutations that generally characterized by dwarfism, reduction in cellulose crystallinity, and reduced root elongation. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2012 journal article

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

MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS, 32(8), 2583–2588.

By: A. Marlowe n, A. Singh n & Y. Yingling n

Contributors: A. Marlowe n, A. Singh n & Y. Yingling n

author keywords: Collagen fibril; Molecular dynamics simulations; Point mutations; Osteogenesis Imperfecta; Mechanical properties
TL;DR: The results suggest that the reduction in mechanical properties of collagen fibrils may be used to predict the clinical outcome of mutations, as well as the trend in reduction of fibril's tensile strength predicted by simulations. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2012 journal article

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

JOURNAL OF MOLECULAR LIQUIDS, 166, 25–30.

By: H. Kim*, R. Pani n, S. Ha*, Y. Koo* & Y. Yingling n

Contributors: H. Kim*, R. Pani n, S. Ha*, Y. Koo* & Y. Yingling n

author keywords: Ionic liquids; Molecular dynamics simulation; Hydrogen bonding; Glucose solubility; Water interactions
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2012 journal article

Tuning DNA structure and compaction with gold nanoparticles

Abstracts of Papers of the American Chemical Society. https://publons.com/publon/28057484/

Contributors: Y. Yingling

Source: ORCID
Added: January 6, 2020

2012 journal article

Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation

ADVANCED MATERIALS, 24(31), 4261-+.

By: J. Railsback n, A. Singh n, R. Pearce n, T. McKnight*, R. Collazo n, Z. Sitar n, Y. Yingling n, A. Melechko n

Contributors: J. Railsback n, A. Singh n, R. Pearce n, T. McKnight*, R. Collazo n, Z. Sitar n, Y. Yingling n, A. Melechko n

author keywords: gold nanoparticles; DNA compaction; DNA denaturing; cationic ligands; DNA-nanoparticle interactions
MeSH headings : Cations / chemistry; DNA / chemistry; Gold / chemistry; Molecular Dynamics Simulation; Nanoparticles / chemistry; Nucleic Acid Conformation; Nucleic Acid Denaturation; Spectrophotometry, Ultraviolet
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2012 article

X3DBio1: A Visual Analysis Tool for Biomolecular Structure Exploration

(P. C. Wong, D. L. Kao, M. C. Hao, C. Chen, R. Kosara, M. A. Livingston, … I. Roberts, Eds.). VISUALIZATION AND DATA ANALYSIS 2012, Vol. 8294.

By: H. Yi, A. Singh n & Y. Yingling n

Ed(s): P. Wong, D. Kao, M. Hao, C. Chen, R. Kosara, M. Livingston, J. Park, I. Roberts

author keywords: molecular visualization; visual analytics; interactive exploration; protein structure; contact map
TL;DR: X3DBio1, a visual analysis tool for 3D biomolecular structure exploration, which allows for easy visual analysis of 2D intra-molecular contact map and 3D density exploration for protein, DNA, and RNA structures, is presented. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2011 journal article

Characterization of Osteogenesis Imperfecta Mutations in Type I Collagen: A Molecular Dynamics Study

Biophysical Journal.

Contributors: Y. Yingling* & A. Marlowe

TL;DR: The results indicate that the lysine mutation dramatically destabilized tropocollagen chemical and mechanical properties, which explains the high death rate related to this mutation. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2011 journal article

Computational Prediction of Cellulose Synthase Protein Structure

Biophysical Journal.

Contributors: Y. Yingling*, L. Sethaphong & A. Vargas

Source: ORCID
Added: January 6, 2020

2011 journal article

Interactions of Cations with RNA Loop-Loop Complexes

BIOPHYSICAL JOURNAL, 101(3), 727–735.

By: A. Singh n, L. Sethaphong n & Y. Yingling n

Contributors: A. Singh n, L. Sethaphong n & Y. Yingling n

MeSH headings : Base Pairing; Base Sequence; Cations / metabolism; Metals / metabolism; Molecular Dynamics Simulation; Nucleic Acid Conformation; RNA / chemistry; RNA / genetics; RNA / metabolism; Solvents / chemistry
TL;DR: Examining interactions of metal ions with five RNA loop-loop complexes of unique biological significance using explicit-solvent molecular-dynamics simulations revealed the presence of solvent-accessible tunnels through the major groove of loop- loop interactions that attract and retain cations. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2011 journal article

Molecular Dynamics Simulation Studies on the Hybridization Events of Surface Immobilized DNA

Biophysical Journal.

Contributors: A. Singh & Y. Yingling*

TL;DR: Simulations suggest that restrained ssDNAs, compared to labile suspensions of free ss DNAs, are more capable of hybridization and hence DNA-based assembly, and this study helps understanding the science associated with the ssDNA hybridization. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: ORCID
Added: January 6, 2020

2011 journal article

Nucleic Acid Helical Conformation and Sequence Effects on Cationic Binding

Biophysical Journal.

Contributors: Y. Yingling* & L. Sethaphong

TL;DR: Molecular dynamics simulations of nucleic acid dupelexes of DNA and RNA were performed to examine subtleties with their inherent cation binding behavior and it is concluded that helical geometry is responsible for a greater majority of cationic interactions and diffusive ion binding than can be explained exclusively by electrostatics resulting from chemical moieties alone. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2011 journal article

Nucleic acid helical conformation and sequence effects on cationic binding

Abstracts of Papers of the American Chemical Society. https://publons.com/publon/28057504/

Contributors: Y. Yingling & L. Sethaphong

Source: ORCID
Added: January 6, 2020

2011 journal article

Simulations of Stretching Single Stranded DNA

MRS Proceedings, 1301.

By: A. Singh n & Y. Yingling n

TL;DR: Simulations suggest that polyA and polyC oligonucleotides exhibit similar force profiles and corresponding elongation, and polyT is the most flexible and needs the most force to unwind from an equilibrium folded structure. (via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2011 article

Theoretical Perspective on Properties of DNA-Functionalized Surfaces

Singh, A., Eksiri, H., & Yingling, Y. G. (2011, November 15). JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, Vol. 49, pp. 1563–1568.

By: A. Singh n, H. Eksiri n & Y. Yingling n

Contributors: Y. Yingling n, H. Eksiri n & A. Singh n

author keywords: DNA-functionalized surface; modeling; nanotechnology; simulations; theory
TL;DR: The understanding of structure and dynamics of DNA immobilized on the surfaces from the theoretical point of view including recent progress in analytical theories, atomistic simulations, and coarse-grained models is discussed. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2010 journal article

Cationic Sequence Dependence in Nucleic Acid Structures

Biophysical Journal.

Contributors: L. Sethaphong n, A. Singh n, A. Marlowe n & Y. Yingling n

TL;DR: Molecular dynamics simulations were performed for a large variety of helical stems to investigate the behavior of cations around nucleic acids and suggest a high propensity toward purine dependent colocalization of one to two cations distinct from those performing phosphate backbone screening. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2010 journal article

Effect of Oligonucleotide Length on the Assembly of DNA Materials: Molecular Dynamics Simulations of Layer-by-Layer DNA Films

LANGMUIR, 26(22), 17339–17347.

By: A. Singh n, S. Snyder n, L. Lee*, A. Johnston*, F. Caruso* & Y. Yingling n

Contributors: Y. Yingling n, F. Caruso*, A. Johnston*, L. Lee*, S. Snyder n & A. Singh n

MeSH headings : Base Sequence; DNA / chemistry; DNA / genetics; Gold / chemistry; Metal Nanoparticles / chemistry; Molecular Dynamics Simulation; Nanotechnology / methods; Nucleic Acid Conformation; Nucleic Acid Hybridization; Oligodeoxyribonucleotides / chemistry; Oligodeoxyribonucleotides / genetics; Poly T / chemistry; Quartz Crystal Microbalance Techniques
TL;DR: This study suggests that restrainedpolyT, compared to labile suspensions of free polyT, are more capable of hybridization and hence DNA-based assembly, and this can be associated with the limited accessibility of the bases on the surface due to formation of self-protected interactions that prevent efficient hybridization. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2010 journal article

Molecular Dynamics and Distribution of Ions in Kissing Loop

Biophysical Journal, 98(3), 264a.

By: A. Singh n, L. Sethaphong n & Y. Yingling n

Contributors: A. Singh n, L. Sethaphong n & Y. Yingling n

TL;DR: It is demonstrated that cations in show strong preferential distribution around kissing loop region however, ion dynamics do not indicate concrete evidence of specific binding, and molecular dynamics results show strong correlation of ionic propensity regulated by sequence. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2010 journal article

The Effect of Genetic Mutations on Structural and Mechanical Properties of Collagen: Molecular Dynamics Simulations

Biophysical Journal, 98(3), 568a.

By: A. Marlowe n & Y. Yingling n

Contributors: Y. Yingling n & A. Marlowe n

TL;DR: The authors' simulations indicate that the mutations significantly affect binding and mechanical properties of the collagen fibrils, and it is predicted that the high death rate related to lysine mutation can be explained by the increase in diameter and significant loss of mechanical properties in collagenfibril. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2010 journal article

The Sequence of HIV-1 TAR RNA Helix Controls Cationic Distribution

JOURNAL OF PHYSICAL CHEMISTRY C, 114(12), 5506–5512.

By: L. Sethaphong n, A. Singh n, A. Marlowe n & Y. Yingling n

Contributors: Y. Yingling n, A. Marlowe n, A. Singh n & L. Sethaphong n

TL;DR: There is a sequence-dependent cationic localization toward the purine-rich run within the TAR helix and other purine -rich duplexes and the behavior is independent of ionic species or a presence of a bulge. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2009 journal article

Computational Discovery Of The Electronegative Channel In RNA Loop-loop Interactions

Biophysical Journal, 96(3), 83a.

By: A. Semichaevsky n, A. Singh n & Y. Yingling n

Contributors: A. Semichaevsky n, A. Singh n & Y. Yingling n

TL;DR: It is discovered that in most organisms the loop-loop assembly process depends on the presence of electronegative and hydration channel and the size of this channel and RNA sequence determines the stability. (via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2009 journal article

Computational and Experimental Determination of the tRNA-like Structure in the 3′UTR of the Turnip Crinkle Virus (TCV)

Biophysical Journal, 96(3), 19a–20a.

By: W. Kasprzak*, Y. Yingling n, A. Simon* & B. Shapiro

TL;DR: The model with its structure-implied functionality has led to further experimental determination of how the interconnected 3′ UTR sequence and structure elements participate in the processes of translation and replication, and the structure element was found to bind the 60S ribosomal subunit, and thus act as a translation enhancer. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Source: ORCID
Added: January 6, 2020

2008 journal article

COMP 215-Explicit molecular dynamics simulations of kissing loop motif formed between TAR-RNA element of HIV-1 and aptamer

Abstracts of Papers of the American Chemical Society. https://publons.com/wos-op/publon/28057500/

Contributors: A. Singh & Y. Yingling

Source: ORCID
Added: January 6, 2020

2008 journal article

Comparing Ion Distributions around RNA and DNA Helical and Loop-loop Motifs

MRS Proceedings, 1130.

By: A. Semichaevsky n, A. Marlowe n & Y. Yingling n

Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2008 chapter

Protocols for the In Silico Design of RNA Nanostructures

In Methods in Molecular Biology™ (pp. 93–115).

By: B. Shapiro*, E. Bindewald*, W. Kasprzak* & Y. Yingling*

Contributors: Y. Yingling*

MeSH headings : Computational Biology / methods; Databases, Genetic; Nanoparticles / chemistry; Nanotechnology / methods; Nucleic Acid Conformation; RNA / chemistry
TL;DR: Presented in this chapter are some methodological shaped-based protocols for the design of such RNA nanostructures that use a database of three-dimensional RNA structure motifs; designed RNA secondary structure motifS; and a combination of the two approaches. (via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2008 journal article

Structural Domains within the 3' Untranslated Region of Turnip Crinkle Virus

Journal of Virology, 82(17), 8706–8720.

By: J. McCormack*, X. Yuan*, Y. Yingling*, W. Kasprzak*, R. Zamora*, B. Shapiro*, A. Simon*

Contributors: J. McCormack*, X. Yuan*, Y. Yingling*, W. Kasprzak*, R. Zamora*, B. Shapiro*, A. Simon*

MeSH headings : 3' Untranslated Regions / chemistry; 3' Untranslated Regions / genetics; Algorithms; Base Pair Mismatch; Base Sequence; Carmovirus / chemistry; Carmovirus / genetics; Computer Simulation; Genes, Viral; Models, Molecular; Molecular Sequence Data; Mutation; Nucleic Acid Conformation; Plasmids; Protein Structure, Tertiary; RNA / chemistry; RNA, Satellite / chemistry; RNA, Viral / biosynthesis; RNA, Viral / chemistry; RNA, Viral / genetics; RNA, Viral / isolation & purification; Virus Replication
TL;DR: A detailed analysis of secondary and tertiary elements within the 3′ end of Turnip crinkle virus that are required for viral accumulation in vivo provides a framework for determining how interconnected elements participate in processes that require 3′ untranslated region sequences such as translation and replication. (via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2008 journal article

The 3' proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits

RNA, 14(11), 2379–2393.

By: V. Stupina*, A. Meskauskas*, J. McCormack*, Y. Yingling*, B. Shapiro*, J. Dinman*, A. Simon*

Contributors: A. Simon*, J. Dinman*, B. Shapiro*, Y. Yingling*, J. McCormack*, A. Meskauskas*, V. Stupina*

author keywords: cap-independent translation; internal ribosome entry site; Turnip crinkle virus; translational enhancer
TL;DR: A strong correlation suggests that ribosome entry in the 3' UTR is a key function of the3' translational enhancer of TCV and that the T-shaped element contains some tRNA-like properties. (via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2007 journal article

Bridging the gap in RNA structure prediction

Current Opinion in Structural Biology, 17(2), 157–165.

By: B. Shapiro*, Y. Yingling*, W. Kasprzak* & E. Bindewald*

Contributors: E. Bindewald*, W. Kasprzak*, Y. Yingling* & B. Shapiro*

MeSH headings : Algorithms; Base Sequence; Computer Simulation; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; RNA / chemistry; RNA / genetics; Sequence Alignment; Software; Thermodynamics
TL;DR: This work bridges the gap between RNA secondary structure prediction, including pseudoknots, and three-dimensional modeling of RNA, and uses this information in conjunction with manual manipulation, constraint satisfaction methods, molecular mechanics and molecular dynamics. (via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2007 journal article

Computational Design of an RNA Hexagonal Nanoring and an RNA Nanotube

Nano Letters, 7(8), 2328–2334.

By: Y. Yingling* & B. Shapiro*

Contributors: B. Shapiro* & Y. Yingling*

MeSH headings : Computer Simulation; Crystallization / methods; Drug Carriers / chemistry; Drug Design; Macromolecular Substances / chemistry; Materials Testing; Models, Chemical; Models, Molecular; Nanostructures / chemistry; Nanostructures / ultrastructure; Nanotechnology / methods; Nucleic Acid Conformation; Particle Size; RNA / chemistry; RNA / ultrastructure; Surface Properties
TL;DR: A computational design of an RNA nanoring and a nanotube is presented, which consists of six simple linear building blocks assembled together via known noncovalent loop-loop contacts based on RNAI/RNAII inverse sequences. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2007 journal article

Computational investigation into the mechanisms of UV ablation of poly(methyl methacrylate)

Applied Surface Science, 253(15), 6382–6385.

By: M. Prasad, P. Conforti, B. Garrison & Y. Yingling*

Contributors: Y. Yingling*, B. Garrison, P. Conforti & M. Prasad

author keywords: computational investigation; mechanisms of UV ablation; poly(methyl methacrylate)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2007 journal article

Computational studies of ultraviolet ablation of poly(methyl methacrylate)

Journal of Physics: Conference Series, 59, 322–327.

By: P. Conforti*, Y. Yingling* & B. Garrison*

Contributors: B. Garrison*, Y. Yingling* & P. Conforti*

Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2007 journal article

Incorporation of chemical reactions into UV photochemical ablation of coarse-grained material

Applied Surface Science, 253(15), 6377–6381.

By: Y. Yingling* & B. Garrison*

Contributors: B. Garrison* & Y. Yingling*

author keywords: laser ablation; simulations; coarse-grained; photochemistry
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2007 journal article

RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign

Nucleic Acids Research, 36(suppl_1), D392–D397.

By: E. Bindewald*, R. Hayes*, Y. Yingling*, W. Kasprzak* & B. Shapiro*

Contributors: B. Shapiro*, W. Kasprzak*, Y. Yingling*, R. Hayes* & E. Bindewald*

MeSH headings : Algorithms; Databases, Nucleic Acid; Internet; Nanostructures / chemistry; Nanotechnology; Nucleic Acid Conformation; RNA / chemistry; Sequence Analysis, RNA; User-Computer Interface
TL;DR: A database that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions and the structural data was subjected to energy minimization. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2007 journal article

The Impact of Dyskeratosis Congenita Mutations on the Structure and Dynamics of the Human Telomerase RNA Pseudoknot Domain

Journal of Biomolecular Structure and Dynamics, 24(4), 303–319.

By: Y. Yingling* & B. Shapiro*

Contributors: B. Shapiro* & Y. Yingling*

author keywords: dyskeratosis congenita; telomerase; RNA; molecular modeling; and pseudoknot
MeSH headings : Base Sequence; Dyskeratosis Congenita / genetics; Humans; Kinetics; Models, Molecular; Molecular Sequence Data; Mutation; Nucleic Acid Conformation; Nucleic Acid Denaturation; RNA / chemistry; RNA / genetics; Software; Telomerase / genetics; Thermodynamics
TL;DR: The results show that the DKC mutations stabilize the hairpin form and destabilize the pseudoknot form of telomerase RNA, and the P3 region of the predicted DKC-mutated pseudok not structure is unstable and fails to form as a defined helical stem. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2007 journal article

Theoretical investigation of formation and properties of RNA nanoparticles

Biophysical Journal. https://publons.com/publon/11561857/

Contributors: Y. Yingling

Source: ORCID
Added: January 6, 2020

2006 journal article

Structural and Dynamical Classification of RNA Single-Base Bulges for Nanostructure Design

Journal of Computational and Theoretical Nanoscience, 3(1), 63–77.

By: W. Hastings, Y. Yingling, G. Chirikjian & B. Shapiro

author keywords: protein NanoActuator; NanoMotor; molecular dynamics; TMD
Sources: Web Of Science, NC State University Libraries
Added: January 14, 2021

2006 journal article

Structural and dynamical classification of RNA single-base bulges for nanostructure design

Journal of Computational and Theoretical Nanoscience.

Contributors: W. Hastings, Y. Yingling, G. Chirikjian & B. Shapiro

author keywords: photon; emission; photoelectron; photon field; radiation; superluminal speeds
Source: ORCID
Added: January 6, 2020

2006 journal article

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(2), 261–274.

By: Y. Yingling* & B. Shapiro

Contributors: Y. Yingling* & B. Shapiro

author keywords: telomerase; RNA; molecular dynamics; theoretical prediction; pseudoknot
MeSH headings : Base Pairing / genetics; Base Sequence; Computer Simulation; Humans; Hydrogen Bonding; Models, Molecular; Nucleic Acid Conformation; RNA / chemistry; RNA / genetics; Telomerase / chemistry; Telomerase / genetics; Thermodynamics
TL;DR: It is shown that the effect of the bulge on the structure results in a significant transformation of the pseudoknot junction region where the starting base pairs are disrupted and unique triple base pairs is formed. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 6, 2020

2005 journal article

Coarse-Grained Model of the Interaction of Light with Polymeric Material: Onset of Ablation

The Journal of Physical Chemistry B, 109(34), 16482–16489.

By: Y. Yingling* & B. Garrison*

Contributors: Y. Yingling* & B. Garrison*

MeSH headings : Light; Models, Molecular; Molecular Conformation; Photochemistry; Polymethyl Methacrylate / chemistry; Thermodynamics; Vibration
TL;DR: A coarse-grained model has been developed for molecular dynamics simulations of the interaction of light with polymeric materials that permits the study of laser ablation, degradation, or the effect of various chemical reactions on large time and length scales. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2005 journal article

Dynamic Behavior of the Telomerase RNA Hairpin Structure and its Relationship to Dyskeratosis Congenita

Journal of Molecular Biology, 348(1), 27–42.

By: Y. Yingling* & B. Shapiro

Contributors: B. Shapiro & Y. Yingling*

author keywords: telomerase; RNA; molecular dynamics simulations; dyskeratosis congenita; pseudoknot
MeSH headings : Base Pairing; Base Sequence; Dyskeratosis Congenita / genetics; Humans; Hydrogen Bonding; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Protein Structure, Secondary; RNA / chemistry; RNA / genetics; RNA / metabolism; Telomerase / chemistry; Telomerase / genetics; Telomerase / metabolism
TL;DR: The results from a comprehensive study of nanosecond-scale implicit and explicit solvent molecular dynamics simulations of the wild-type telomerase RNA hairpin suggest a possible mechanism for pseudoknot formation based on the dynamics of the hairpin structure and also may explain the mutational aspects of dyskeratosis congenita. (via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2004 journal article

Coarse-Grained Chemical Reaction Model

The Journal of Physical Chemistry B, 108(6), 1815–1821.

By: Y. Yingling* & B. Garrison*

Contributors: B. Garrison* & Y. Yingling*

TL;DR: The new coarse-grained chemical reaction model (CGCRM) adopts the philosophy of kinetic Monte Carlo approaches and includes a probabilistic element to predicting when reactions occur, thus obviating the need for a chemically correct interaction potential. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 6, 2020

2004 journal article

Theoretical investigation of laser pulse width dependence in a thermal confinement regime

Applied Physics A, 79(4-6), 757–759.

By: Y. Yingling*, P. Conforti* & B. Garrison*

Contributors: B. Garrison*, P. Conforti* & Y. Yingling*

Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2003 journal article

Big molecule ejection—SIMS vs. MALDI

Applied Surface Science, 203-204, 69–71.

By: B. Garrison*, A. Delcorte*, L. Zhigilei*, T. Itina*, K. Krantzman*, Y. Yingling*, C. McQuaw*, E. Smiley*, N. Winograd*

Contributors: B. Garrison*, A. Delcorte*, L. Zhigilei*, T. Itina*, K. Krantzman*, Y. Yingling*, C. McQuaw*, E. Smiley*, N. Winograd*

author keywords: MALDI; organic SIMS; molecular dynamics; computer simulation
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2003 journal article

Computer Simulations of Laser Ablation of Molecular Substrates

ChemInform, 34(18).

By: L. Zhigilei*, E. Leveugle*, B. Garrison*, Y. Yingling* & M. Zeifman*

Source: ORCID
Added: January 6, 2020

2003 journal article

Computer Simulations of Laser Ablation of Molecular Substrates

Chemical Reviews, 103(2), 321–348.

By: L. Zhigilei*, E. Leveugle*, B. Garrison, Y. Yingling* & M. Zeifman*

Contributors: M. Zeifman*, Y. Yingling*, B. Garrison, E. Leveugle* & L. Zhigilei*

TL;DR: Computer Simulations of Laser Ablation of Molecular Substrates Chemical Reviews, 2003, Vol. (via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2003 journal article

Molecular dynamics simulations of matrix-assisted laser desorption - connections to experiment

International Journal of Mass Spectrometry, 226(1), 85–106.

By: L. Zhigilei*, Y. Yingling*, T. Itina*, T. Schoolcraft* & B. Garrison*

Contributors: B. Garrison*, T. Schoolcraft*, T. Itina*, Y. Yingling* & L. Zhigilei*

author keywords: ablation; MALDI; molecular dynamics
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 6, 2020

2003 journal article

Photochemical ablation of organic solids

Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 202, 188–194.

By: Y. Yingling* & B. Garrison*

Contributors: B. Garrison* & Y. Yingling*

author keywords: molecular dynamics simulations; laser ablation; photochemical fragmentation; photochemical processes
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2002 journal article

Photochemical induced effects in material ejection in laser ablation

Chemical Physics Letters, 364(3-4), 237–243.

By: Y. Yingling* & B. Garrison*

Contributors: Y. Yingling* & B. Garrison*

Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2001 journal article

Laser ablation of bicomponent systems: A probe of molecular ejection mechanisms

Applied Physics Letters, 78(11), 1631–1633.

By: Y. Yingling*, L. Zhigilei*, B. Garrison*, A. Koubenakis*, J. Labrakis* & S. Georgiou*

Contributors: Y. Yingling*, L. Zhigilei*, B. Garrison*, A. Koubenakis*, J. Labrakis* & S. Georgiou*

Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2001 journal article

Photochemical fragmentation processes in laser ablation of organic solids

Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 180(1-4), 171–175.

By: Y. Yingling*, L. Zhigilei* & B. Garrison*

Contributors: Y. Yingling*, L. Zhigilei* & B. Garrison*

author keywords: molecular dynamics simulations; laser ablation; photofragmentation
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

2001 journal article

The role of the photochemical fragmentation in laser ablation: a molecular dynamics study

Journal of Photochemistry and Photobiology A: Chemistry, 145(3), 173–181.

By: Y. Yingling*, L. Zhigilei* & B. Garrison*

Contributors: Y. Yingling*, L. Zhigilei* & B. Garrison*

author keywords: photochemical fragmentation; laser ablation; molecular dynamics
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: January 6, 2020

journal article

New polyvalent RNA nanoparticle comprises RNA motifs as building blocks, useful in a drug delivery composition for treating or preventing a disease or disorder, e.g. AIDS, Alzheimer's disease, anemia, cancer, hypertension, or obesity

https://publons.com/publon/15543588/

Contributors: Y. Yingling

Source: ORCID
Added: January 6, 2020

journal article

New polyvalent RNA nanoparticle, useful for treating or preventing a disease or disorder, e.g. adenoma, aging, AIDS, alopecia, Alzheimer's disease, or anemia

https://publons.com/publon/15543587/

Contributors: Y. Yingling

Source: ORCID
Added: January 6, 2020

Employment

Updated: April 4th, 2022 10:08

2007 - present

NC State University Raleigh, NC, US
Distinguished Professor Materials Science and Engineering

2004 - 2007

National Cancer Institute Frederick, MD, US
CRTA Fellow Center for Cancer Research Nanobiology Program

2002 - 2004

Pennsylvania State University University Park, PA, US
Postdoctoral Research Associate Chemistry

Education

Updated: December 10th, 2019 21:21

1997 - 2002

Pennsylvania State University University Park, PA, US
PhD Materials

1990 - 1996

Saint Petersburg State Polytechnical University Saint Petersburg, RU
B.S. Computer Science and Engineering

Funding History

Funding history based on the linked ORCID record. Updated: February 25th, 2018 12:01

grant August 1, 2017 - July 31, 2020
Collaborative Research: Processing Films from Multi-Functional Polymer Dispersion Blends
Directorate for Engineering
grant July 15, 2014 - June 30, 2018
Collaborative Research: Supramolecular Materials by Nucleic Acid Block Copolymer Self-Assembly
Directorate for Mathematical & Physical Sciences
grant July 15, 2014 - June 30, 2017
Collaborative Research: Supramolecular Materials by Nucleic Acid Block Copolymer Self-Assembly
National Science Foundation
grant July 1, 2014 - June 30, 2018
Confinement, Dynamics, and Orientation of DNA at Nano-interfaces
Directorate for Engineering
grant July 1, 2014 - June 30, 2017
Confinement, Dynamics, and Orientation of DNA at Nano-interfaces
National Science Foundation
grant September 1, 2013 - May 31, 2014
Modeling and Theory-Driven Design of Soft Materials
Directorate for Mathematical & Physical Sciences
grant September 1, 2013 - May 31, 2014
Modeling and Theory-Driven Design of Soft Materials
National Science Foundation
grant June 1, 2012 - June 30, 2018
Texas State University PREM: Center on Interfaces in Materials. A Partnership with the Research Triangle MRSEC
Directorate for Mathematical & Physical Sciences
grant June 1, 2012 - May 31, 2017
Texas State University PREM: Center on Interfaces in Materials. A Partnership with the Research Triangle MRSEC
National Science Foundation
grant February 15, 2012 - January 31, 2018
CAREER: Integrating DNA and Inorganic Surfaces for Functional Materials Design
Directorate for Engineering
grant February 15, 2012 - January 31, 2017
CAREER: Integrating DNA and Inorganic Surfaces for Functional Materials Design
National Science Foundation
grant May 1, 2010 - April 30, 2014
Magnetically-Driven Orientation of Multiphase Polymer Systems: A Ligand-Functionalized, Magnetic Nanoparticle Approach
Directorate for Engineering
grant May 1, 2010 - April 30, 2014
Magnetically-Driven Orientation of Multiphase Polymer Systems: A Ligand-Functionalized, Magnetic Nanoparticle Approach
National Science Foundation

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