@article{kwansa_singh_williams_haigler_roberts_yingling_2024, title={Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods}, volume={1}, ISSN={["1572-882X"]}, DOI={10.1007/s10570-023-05691-x}, journal={CELLULOSE}, author={Kwansa, Albert L. and Singh, Abhishek and Williams, Justin T. and Haigler, Candace H. and Roberts, Alison W. and Yingling, Yaroslava G.}, year={2024}, month={Jan} }
 @article{du_vandavasi_molloy_yang_massenburg_singh_kwansa_yingling_o'neill_chait_et al._2022, title={Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes br}, volume={8}, ISSN={["1526-4602"]}, url={https://doi.org/10.1021/acs.biomac.2c00550}, DOI={10.1021/acs.biomac.2c00550}, abstractNote={Higher plants synthesize cellulose using membrane-bound, six-lobed cellulose synthase complexes, each lobe containing trimeric cellulose synthases (CESAs). Although molecular biology reports support heteromeric trimers composed of different isoforms, a homomeric trimer was reported for in vitro studies of the catalytic domain of CESA1 of Arabidopsis (AtCESA1CatD) and confirmed in cryoEM structures of full-length CESA8 and CESA7 of poplar and cotton, respectively. In both structures, a small portion of the plant-conserved region (P-CR) forms the only contacts between catalytic domains of the monomers. We report inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD. Molecular dynamics simulations for AtCESA1CatD trimers based on the CESA8 cryoEM structure were stable and dependent upon a small set of residue contacts. The results 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.}, journal={BIOMACROMOLECULES}, publisher={American Chemical Society (ACS)}, author={Du, Juan and Vandavasi, Venu Gopal and Molloy, Kelly R. and Yang, Hui and Massenburg, Lynnicia N. and Singh, Abhishek and Kwansa, Albert L. and Yingling, Yaroslava G. and O'Neill, Hugh and Chait, Brian T. and et al.}, year={2022}, month={Aug} }
 @article{oweida_kim_donald_singh_yingling_2021, title={Assessment of AMBER Force Fields for Simulations of ssDNA}, volume={17}, ISSN={["1549-9626"]}, url={https://doi.org/10.1021/acs.jctc.0c00931}, DOI={10.1021/acs.jctc.0c00931}, abstractNote={Single-stranded DNA (ssDNA) plays an important role in biological processes and is used in DNA nanotechnology and other novel applications. Many important research questions can be addressed with molecular simulations of ssDNA molecules; however, no dedicated force field for ssDNA has been developed, and there is limited experimental information about ssDNA structures. This study assesses the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, such as ff99, bsc0, bsc1, and OL15, in implicit and explicit solvents via comparison to available experimental data, such as Forster resonance energy transfer and small angle X-ray scattering. We observed 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. Overall, the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experiment.}, number={2}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, publisher={American Chemical Society (ACS)}, author={Oweida, Thomas J. and Kim, Ho Shin and Donald, Johnny M. and Singh, Abhishek and Yingling, Yaroslava G.}, year={2021}, month={Feb}, pages={1208–1217} }
 @article{burris_makarem_slabaugh_chaves_pierce_lee_kiemle_kwansa_singh_yingling_et al._2021, title={Phenotypic effects of changes in the FTVTxK region of an Arabidopsis secondary wall cellulose synthase compared with results from analogous mutations in other isoforms}, volume={5}, ISSN={["2475-4455"]}, url={https://doi.org/10.1002/pld3.335}, DOI={10.1002/pld3.335}, abstractNote={Understanding protein structure and function relationships in cellulose synthase (CesA), including divergent isomers, is an important goal. Here, we report results from mutant complementation assays that tested the ability of sequence variants of AtCesA7, a secondary wall CesA of Arabidopsis thaliana, to rescue the collapsed vessels, short stems, and low cellulose content of the irx3-1 AtCesA7 null mutant. We tested a catalytic null mutation and seven missense or small domain changes in and near the AtCesA7 FTVTSK motif, which lies near the catalytic domain and may, analogously to bacterial CesA, exist within a substrate "gating loop." A low-to-high gradient of rescue occurred, and even inactive AtCesA7 had a small positive effect on stem cellulose content but not stem elongation. Overall, secondary wall cellulose content and stem length were moderately correlated, but the results were consistent with threshold amounts of cellulose supporting particular developmental processes. Vibrational sum frequency generation microscopy allowed tissue-specific analysis of cellulose content in stem xylem and interfascicular fibers, revealing subtle differences between selected genotypes that correlated with the extent of rescue of the collapsing xylem phenotype. Similar tests on PpCesA5 from the moss Physcomitrium (formerly Physcomitrella) patens helped us to synergize the AtCesA7 results with prior results on AtCesA1 and PpCesA5. 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.}, number={8}, journal={PLANT DIRECT}, publisher={Wiley}, author={Burris, Jason N. and Makarem, Mohamadamin and Slabaugh, Erin and Chaves, Arielle and Pierce, Ethan T. and Lee, Jongcheol and Kiemle, Sarah N. and Kwansa, Albert L. and Singh, Abhishek and Yingling, Yaroslava G. and et al.}, year={2021}, month={Aug} }
 @article{lee_stryutsky_mahmood_singh_shevchenko_yingling_tsukruk_2021, title={Weakly Ionically Bound Thermosensitive Hyperbranched Polymers}, volume={37}, ISSN={["0743-7463"]}, DOI={10.1021/acs.langmuir.0c03487}, abstractNote={We synthesized novel amphiphilic hyperbranched polymers (HBPs) with variable contents of weakly ionically tethered thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) macrocations in contrast to traditional covalent linking. Their assembling behavior was studied below and above the lower critical solution temperature (LCST). The HBPs underwent a morphological transition under changing temperature and ionic strength due to the LCST transition of PNIPAM and the reduction in the ionization degree of terminal ionic groups, respectively. We suggest 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. In addition, assembly at the air-water interface confined PNIPAM macrocations and resulted in the formation of heterogeneous Langmuir-Blodgett (LB) monolayers with diverse surface morphologies for different peripheral compositions with circular domains formed in the condensed state. The HBPs with 25% PNIPAM showed larger and more stable circular domains that were partially preserved at high compression than those of HBPs with 50% PNIPAM. Moreover, the LB monolayers showed variable surface mechanical and surface charge distribution, which can be attributed to net dipole redistribution caused by the behavior of mobile PNIPAM macrocations and core sulfonate groups.}, number={9}, journal={LANGMUIR}, author={Lee, Hansol and Stryutsky, Alexandr and Mahmood, Akhlak-Ul and Singh, Abhishek and Shevchenko, Valery V. and Yingling, Yaroslava G. and Tsukruk, Vladimir V.}, year={2021}, month={Mar}, pages={2913–2927} }
 @article{mcgoorty_singh_deaton_peterson_taliaferro_yingling_castellano_2018, title={Bathophenanthroline Disulfonate Ligand-Induced Self-Assembly of Ir(III) Complexes in Water: An Intriguing Class of Photoluminescent Soft Materials}, volume={3}, ISSN={2470-1343 2470-1343}, url={http://dx.doi.org/10.1021/acsomega.8b02034}, DOI={10.1021/acsomega.8b02034}, abstractNote={Strong evidence of concentration-induced and dissolved electrolyte-induced chromophore aggregation has been universally observed in numerous water soluble bis-cyclometalated Ir(III) photosensitizers bearing the sulfonated diimine ligands bathophenanthroline disulfonate and bathocuproine disulfonate. This new class of aqueous-based soft materials was highly photoluminescent in their aggregated state where detailed spectroscopic investigations of this phenomenon revealed significant blue shifts of their respective photoluminescence emission spectra with concomitant increases in excited-state lifetimes and quantum yields initiating even at micromolar chromophore concentrations in water or upon the addition of a strong electrolyte. A combination of nanoscale particle characterization techniques, static and dynamic photoluminescence spectroscopic studies, along with atomistic molecular dynamics (MD) 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. Importantly, the experimental and MD findings suggest the likelihood of discovering similar aqueous aggregation phenomena occurring in all transition-metal complexes bearing these water-solubilizing diimine ligands.}, number={10}, journal={ACS Omega}, publisher={American Chemical Society (ACS)}, author={McGoorty, Michelle M. and Singh, Abhishek and Deaton, Thomas A. and Peterson, Benjamin and Taliaferro, Chelsea M. and Yingling, Yaroslava G. and Castellano, Felix N.}, year={2018}, month={Oct}, pages={14027–14038} }
 @article{scavuzzo-duggan_chaves_singh_sethaphong_slabaugh_yingling_haigler_roberts_2018, title={Cellulose synthase "class specific regions' are intrinsically disordered and functionally undifferentiated}, volume={60}, ISSN={["1744-7909"]}, url={https://publons.com/wos-op/publon/28057448/}, DOI={10.1111/jipb.12637}, abstractNote={Cellulose synthases (CESAs) are glycosyltransferases that catalyze formation of cellulose microfibrils in plant cell walls. Seed plant CESA isoforms cluster in six phylogenetic clades, whose non-interchangeable members play distinct roles within cellulose synthesis complexes (CSCs). A 'class specific region' (CSR), with higher sequence similarity within versus between functional CESA classes, has been suggested to contribute to specific activities or interactions of different isoforms. We investigated CESA isoform specificity in the moss, Physcomitrella patens (Hedw.) B. S. G. to gain evolutionary insights into CESA structure/function relationships. Like seed plants, P. patens has oligomeric rosette-type CSCs, but the PpCESAs diverged independently and form a separate CESA clade. We showed that P. patens has two functionally distinct CESAs classes, based on the ability to complement the gametophore-negative phenotype of a ppcesa5 knockout line. Thus, non-interchangeable CESA classes evolved separately in mosses and seed plants. However, testing of chimeric moss CESA genes for complementation demonstrated that functional class-specificity is not determined by the CSR. 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.}, number={6}, journal={JOURNAL OF INTEGRATIVE PLANT BIOLOGY}, publisher={Wiley-Blackwell}, author={Scavuzzo-Duggan, Tess R. and Chaves, Arielle M. and Singh, Abhishek and Sethaphong, Latsavongsakda and Slabaugh, Erin and Yingling, Yaroslava G. and Haigler, Candace H. and Roberts, Alison W.}, year={2018}, month={Jun}, pages={481–497} }
 @article{manning_kwansa_oweida_peerless_singh_yingling_2018, title={Progress in ligand design for monolayer-protected nanoparticles for nanobio interfaces}, volume={13}, ISSN={1934-8630 1559-4106}, url={http://dx.doi.org/10.1116/1.5044381}, DOI={10.1116/1.5044381}, abstractNote={Ligand-functionalized inorganic nanoparticles, also known as monolayer-protected nanoparticles, offer great potential as vehicles for in vivo delivery of drugs, genes, and other therapeutics. These nanoparticles offer highly customizable chemistries independent of the size, shape, and functionality imparted by the inorganic core. Their success as drug delivery agents depends on their interaction with three major classes of biomolecules: nucleic acids, proteins, and membranes. Here, the authors discuss recent advances and open questions in the field of nanoparticle ligand design for nanomedicine, with a focus on atomic-scale interactions with biomolecules. While the importance of charge and hydrophobicity of ligands for biocompatibility and cell internalization has been demonstrated, ligand length, flexibility, branchedness, and other properties also influence the properties of nanoparticles. However, 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.}, number={6}, journal={Biointerphases}, publisher={American Vacuum Society}, author={Manning, Matthew D. and Kwansa, Albert L. and Oweida, Thomas and Peerless, James S. and Singh, Abhishek and Yingling, Yaroslava G.}, year={2018}, month={Dec}, pages={06D502} }
 @article{nagarajan_rongala_luang_singh_shadiac_hayes_sutton_gilliham_tyerman_mcphee_et al._2016, title={A Barley Efflux Transporter Operates in a Na+-Dependent Manner, as Revealed by a Multidisciplinary Platform}, volume={28}, ISSN={["1532-298X"]}, url={https://publons.com/wos-op/publon/5454554/}, DOI={10.1105/tpc.15.00625}, abstractNote={A barley efflux transporter that is primarily borate-permeable operates as a channel in a Na+-dependent manner. Plant growth and survival depend upon the activity of membrane transporters that control the movement and distribution of solutes into, around, and out of plants. Although many plant transporters are known, their intrinsic properties make them difficult to study. In barley (Hordeum vulgare), the root anion-permeable transporter Bot1 plays a key role in tolerance to high soil boron, facilitating the efflux of borate from cells. However, its three-dimensional structure is unavailable and the molecular basis of its permeation function is unknown. Using an integrative platform of computational, biophysical, and biochemical tools as well as molecular biology, electrophysiology, and bioinformatics, we provide insight into the origin of transport function of Bot1. An atomistic model, supported by atomic force microscopy measurements, reveals that the protein folds into 13 transmembrane-spanning and five cytoplasmic α-helices. We predict a trimeric assembly of Bot1 and the presence of a Na+ ion binding site, located in the proximity of a pore that conducts anions. Patch-clamp electrophysiology of Bot1 detects Na+-dependent polyvalent anion transport in a Nernstian manner with channel-like characteristics. Using alanine scanning, molecular dynamics simulations, and transport measurements, we show that conductance by Bot1 is abolished by removal of the Na+ ion binding site. Our data enhance the understanding of the permeation functions of Bot1.}, number={1}, journal={Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Nagarajan, Yagnesh and Rongala, Jay and Luang, Sukanya and Singh, Abhishek and Shadiac, Nadim and Hayes, Julie and Sutton, Tim and Gilliham, Matthew and Tyerman, Stephen and McPhee, Gordon and et al.}, year={2016}, pages={202–218} }
 @article{nixon_mansouri_singh_du_davis_lee_slabaugh_vandavasi_o’neill_roberts_et al._2016, title={Comparative Structural and Computational Analysis Supports Eighteen Cellulose Synthases in the Plant Cellulose Synthesis Complex}, volume={6}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/srep28696}, DOI={10.1038/srep28696}, abstractNote={A six-lobed membrane spanning cellulose synthesis complex (CSC) containing multiple cellulose synthase (CESA) glycosyltransferases mediates cellulose microfibril formation. The number of CESAs in the CSC has been debated for decades in light of changing estimates of the diameter of the smallest microfibril formed from the β-1,4 glucan chains synthesized by one CSC. We obtained more direct evidence through generating improved transmission electron microscopy (TEM) images and image averages of the rosette-type CSC, revealing the frequent triangularity and average cross-sectional area in the plasma membrane of its individual lobes. Trimeric oligomers of two alternative CESA computational models corresponded well with individual lobe geometry. A six-fold assembly of the trimeric computational oligomer had the lowest potential energy per monomer and was consistent with rosette CSC morphology. Negative stain TEM and image averaging showed the triangularity of a recombinant CESA cytosolic domain, consistent with previous modeling of its trimeric nature from small angle scattering (SAXS) data. Six trimeric SAXS models nearly filled the space below an average FF-TEM image of the rosette CSC. In summary, the multifaceted data support a rosette CSC with 18 CESAs that mediates the synthesis of a fundamental microfibril composed of 18 glucan chains.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Nixon, B. Tracy and Mansouri, Katayoun and Singh, Abhishek and Du, Juan and Davis, Jonathan K. and Lee, Jung-Goo and Slabaugh, Erin and Vandavasi, Venu Gopal and O’Neill, Hugh and Roberts, Eric M. and et al.}, year={2016}, month={Jun} }
 @article{sethaphong_davis_slabaugh_singh_haigler_yingling_2016, title={Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis}, volume={23}, ISSN={0969-0239 1572-882X}, url={http://dx.doi.org/10.1007/s10570-015-0789-6}, DOI={10.1007/s10570-015-0789-6}, number={1}, journal={Cellulose}, publisher={Springer Science and Business Media LLC}, author={Sethaphong, Latsavongsakda and Davis, Jonathan K. and Slabaugh, Erin and Singh, Abhishek and Haigler, Candace H. and Yingling, Yaroslava G.}, year={2016}, month={Feb}, pages={145–161} }
 @article{lei_singh_bashline_li_yingling_gu_2015, title={CELLULOSE SYNTHASE INTERACTIVE1 Is Required for Fast Recycling of Cellulose Synthase Complexes to the Plasma Membrane in Arabidopsis}, volume={27}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.15.00442}, DOI={10.1105/tpc.15.00442}, abstractNote={Rapid recycling of cellulose synthase in plants under stress is dependent on CELLULOSE SYNTHASE INTERACTIVE1- and clathrin-mediated endocytosis. Plants are constantly subjected to various biotic and abiotic stresses and have evolved complex strategies to cope with these stresses. For example, plant cells endocytose plasma membrane material under stress and subsequently recycle it back when the stress conditions are relieved. Cellulose biosynthesis is a tightly regulated process that is performed by plasma membrane-localized cellulose synthase (CESA) complexes (CSCs). However, the regulatory mechanism of cellulose biosynthesis under abiotic stress has not been well explored. In this study, we show that small CESA compartments (SmaCCs) or microtubule-associated cellulose synthase compartments (MASCs) are critical for fast recovery of CSCs to the plasma membrane after stress is relieved in Arabidopsis thaliana. This SmaCC/MASC-mediated fast recovery of CSCs is dependent on CELLULOSE SYNTHASE INTERACTIVE1 (CSI1), a protein previously known to represent the link between CSCs and cortical microtubules. Independently, AP2M, a core component in clathrin-mediated endocytosis, plays a role in the formation of SmaCCs/MASCs. Together, our 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.}, number={10}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Lei, Lei and Singh, Abhishek and Bashline, Logan and Li, Shundai and Yingling, Yaroslava G. and Gu, Ying}, year={2015}, month={Oct}, pages={tpc.15.00442} }
 @article{nash_singh_li_yingling_2015, title={Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics}, volume={9}, ISSN={["1936-086X"]}, url={https://publons.com/publon/5454552/}, DOI={10.1021/acsnano.5b05684}, abstractNote={The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our 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. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.}, number={12}, journal={ACS NANO}, publisher={American Chemical Society (ACS)}, author={Nash, Jessica A. and Singh, Abhishek and Li, Nan K. and Yingling, Yaroslava G.}, year={2015}, month={Dec}, pages={12374–12382} }
 @article{marlowe_singh_yingling_2012, title={The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study}, volume={32}, ISSN={["1873-0191"]}, url={https://publons.com/wos-op/publon/11561894/}, DOI={10.1016/j.msec.2012.07.044}, abstractNote={Understanding sequence dependent mechanical and structural properties of collagen fibrils is important for the development of artificial biomaterials for medical and nanotechnological applications. Moreover, point mutations are behind many collagen associated diseases, including Osteogenesis Imperfecta (OI). We conducted a combination of classical and steered atomistic molecular dynamics simulations to examine the effect of point mutations on structure and mechanical properties of short collagen fibrils which include mutations of glycine to alanine, aspartic acid, cysteine, and serine or mutations of hydroxyproline to arginine, asparagine, glutamine, and lysine. We found that all mutations disrupt structure and reduce strength of the collagen fibrils, which may affect the hierarchical packing of the fibrils. The glycine mutations were more detrimental to mechanical strength of the fibrils (WT > Ala > Ser > Cys > Asp) than that of hydroxyproline (WT > Arg > Gln > Asn > Lys). The clinical outcome for glycine mutations agrees well with the trend in reduction of fibril's tensile strength predicted by our simulations. Overall, our results suggest that the reduction in mechanical properties of collagen fibrils may be used to predict the clinical outcome of mutations.}, number={8}, journal={MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS}, publisher={Elsevier BV}, author={Marlowe, Ashley E. and Singh, Abhishek and Yingling, Yaroslava G.}, year={2012}, month={Dec}, pages={2583–2588} }
 @article{railsback_singh_pearce_mcknight_collazo_sitar_yingling_melechko_2012, title={Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation}, volume={24}, ISSN={["0935-9648"]}, url={https://publons.com/wos-op/publon/5454547/}, DOI={10.1002/adma.201104891}, abstractNote={Weakly charged cationic nanoparticles cause structural changes including local denaturing and compaction to DNA under mild conditions. The charged ligands bind to the phosphate backbone of DNA and the uncharged ligands penetrate the helix and disrupt base pairing. Mobility shifts in electrophoresis, molecular dynamics, and UV-vis spectrophotometry give clues to the details of the interactions.}, number={31}, journal={ADVANCED MATERIALS}, publisher={Wiley-Blackwell}, author={Railsback, Justin G. and Singh, Abhishek and Pearce, Ryan C. and McKnight, Timothy E. and Collazo, Ramon and Sitar, Zlatko and Yingling, Yaroslava G. and Melechko, Anatoli V.}, year={2012}, month={Aug}, pages={4261-+} }
 @article{yi_singh_yingling_2012, title={X3DBio1: A Visual Analysis Tool for Biomolecular Structure Exploration}, volume={8294}, ISSN={["1996-756X"]}, url={https://publons.com/publon/10869587/}, DOI={10.1117/12.906893}, abstractNote={Protein tertiary structure analysis provides valuable information on their biochemical functions. The structure-to-function 
relationship can be directly addressed through three dimensional (3D) biomolecular structure exploration and 
comparison. We present 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. A case study is also presented in this paper to illustrate the utility of the tool. X3DBio1 is open source and 
freely downloadable. We expect this tool can be applied to solve a variety of biological problems.}, journal={VISUALIZATION AND DATA ANALYSIS 2012}, publisher={SPIE}, author={Yi, Hong and Singh, Abhishek and Yingling, Yaroslava G.}, editor={Wong, Pak Chung and Kao, David L. and Hao, Ming C. and Chen, Chaomei and Kosara, Robert and Livingston, Mark A. and Park, Jinah and Roberts, IanEditors}, year={2012} }
 @article{singh_sethaphong_yingling_2011, title={Interactions of Cations with RNA Loop-Loop Complexes}, volume={101}, ISSN={["0006-3495"]}, url={https://publons.com/publon/5454556/}, DOI={10.1016/j.bpj.2011.06.033}, abstractNote={RNA loop-loop interactions are essential in many biological processes, including initiation of RNA folding into complex tertiary shapes, promotion of dimerization, and viral replication. In this article, we examine interactions of metal ions with five RNA loop-loop complexes of unique biological significance using explicit-solvent molecular-dynamics simulations. These simulations revealed the presence of solvent-accessible tunnels through the major groove of loop-loop interactions that attract and retain cations. Ion dynamics inside these loop-loop complexes were distinctly different from the dynamics of the counterion cloud surrounding RNA and depend on the number of basepairs between loops, purine sequence symmetry, and presence of unpaired nucleotides. The cationic uptake by kissing loops depends on the number of basepairs between loops. It is interesting that loop-loop complexes with similar functionality showed similarities in cation dynamics despite differences in sequence and loop size.}, number={3}, journal={BIOPHYSICAL JOURNAL}, publisher={Elsevier BV}, author={Singh, Abhishek and Sethaphong, Latsavongsakda and Yingling, Yaroslava G.}, year={2011}, month={Aug}, pages={727–735} }
 @article{singh_eksiri_yingling_2011, title={Theoretical Perspective on Properties of DNA-Functionalized Surfaces}, volume={49}, ISSN={["0887-6266"]}, url={https://publons.com/publon/5454555/}, DOI={10.1002/polb.22349}, abstractNote={The molecular recognition properties of DNA gave rise to many novel materials and applications such as DNA biosensors, DNA-functionalized colloidal materials, DNA origami and DNA-based directed surface assembly. The DNA-functionalized surfaces are used in biosensors and for programmed self-assembly of biological, organic and inorganic moieties into novel materials. However, surface density, length, and linker design of the surface functionalized DNAs significantly influence the properties of DNA-driven assemblies and materials. This perspective discusses 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. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1563–1568, 2011}, number={22}, journal={JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS}, publisher={Wiley-Blackwell}, author={Singh, Abhishek and Eksiri, Hamed and Yingling, Yaroslava G.}, year={2011}, month={Nov}, pages={1563–1568} }
 @article{singh_snyder_lee_johnston_caruso_yingling_2010, title={Effect of Oligonucleotide Length on the Assembly of DNA Materials: Molecular Dynamics Simulations of Layer-by-Layer DNA Films}, volume={26}, ISSN={["0743-7463"]}, url={https://publons.com/publon/5454528/}, DOI={10.1021/la102762t}, abstractNote={DNA strand length has been found to be an important factor in many DNA-based nanoscale systems. Here, we apply molecular dynamics simulations in a synergistic effort with layer-by-layer experimental data to understand the effect of DNA strand length on the assembly of DNA films. The results indicate that short (less than 10 bases) and long (more than 30 bases) single-stranded DNAs do not exhibit optimal film growth, 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. Interestingly, the presence of a duplex attached to a single strand significantly alters the persistence length of the polyT strands. Our study suggests that restrained polyT, compared to labile suspensions of free polyT, are more capable of hybridization and hence DNA-based assembly.}, number={22}, journal={LANGMUIR}, publisher={American Chemical Society (ACS)}, author={Singh, Abhishek and Snyder, Stacy and Lee, Lillian and Johnston, Angus P. R. and Caruso, Frank and Yingling, Yaroslava G.}, year={2010}, month={Nov}, pages={17339–17347} }
 @article{sethaphong_singh_marlowe_yingling_2010, title={The Sequence of HIV-1 TAR RNA Helix Controls Cationic Distribution}, volume={114}, ISSN={["1932-7455"]}, url={https://publons.com/publon/5454532/}, DOI={10.1021/jp906147q}, abstractNote={Sequence dependency of metal ion aggregation around RNA structures is known to be involved in critical functions ranging from processes of molecular recognition to enzymatic chemistry. Ion interactions with an HIV-1 TAR RNA core helix were examined with explicit solvent molecular dynamics simulations. The results have shown that there is a sequence-dependent cationic localization toward the purine-rich run within the TAR helix and other purine-rich duplexes. The behavior is independent of ionic species or a presence of a bulge. A region of high ion affinity agrees very well with the position of the X-ray determined divalent cations within a fragment from the HIV-1 TAR RNA.}, number={12}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, publisher={American Chemical Society (ACS)}, author={Sethaphong, Latsavongsakda and Singh, Abhishek and Marlowe, Ashley E. and Yingling, Yaroslava G.}, year={2010}, month={Apr}, pages={5506–5512} }