@article{huang_green_huang_hallen_han_lim_2022, title={Room-temperature upconverted superfluorescence}, volume={8}, ISSN={["1749-4893"]}, url={http://dx.doi.org/10.1038/s41566-022-01060-5}, DOI={10.1038/s41566-022-01060-5}, journal={NATURE PHOTONICS}, publisher={Springer Science and Business Media LLC}, author={Huang, Kai and Green, Kory Kevin and Huang, Ling and Hallen, Hans and Han, Gang and Lim, Shuang Fang}, year={2022}, month={Aug} }
 @article{huang_li_li_yu_gao_huang_lim_han_2021, title={Three-Dimensional Colloidal Controlled Growth of Core-Shell Heterostructured Persistent Luminescence Nanocrystals}, volume={21}, ISSN={["1530-6992"]}, DOI={10.1021/acs.nanolett.0c04940}, abstractNote={Persistent luminescence nanoparticles (PLNPs) are an emerging photonic nanomaterial that possesses uniquely persistent luminescence properties after excitation ceases. They can be repeatedly recharged in vitro and in vivo and hold great promise for numerous areas and applications. Unfortunately, none of the existing synthesis methods can control their composition to grow core-shell structured PLNPs with desirable shapes and enhanced functionalities. Here, we report on straightforward thermolysis-mediated colloidal synthesis of CaF2:Dy@NaYF4 core-shell PLNPs that can enhance persistent luminescence under both light and X-ray excitations. Benefitting from the well-matched crystal lattices between CaF2 and NaYF4, this colloidal synthesis makes it possible to prepare core-shell PLNPs with exquisite control of the compositions, shapes, and enhanced luminescence. This demonstration of the developing colloidal core-shell PLNPs overcomes the current key bottleneck regarding the synthesis of heterostructured PLNPs and sets the stage for fully exploiting the potential of these fascinating luminous materials.}, number={12}, journal={NANO LETTERS}, author={Huang, Kai and Li, Zhanjun and Li, Yang and Yu, Nuo and Gao, Xiuping and Huang, Ling and Lim, Shuang Fang and Han, Gang}, year={2021}, month={Jun}, pages={4903–4910} }
 @article{meiling_monks_huang_meng_chen_zhou_lim_würth_resch-genger_chen_2020, title={Efficient sub-15 nm cubic-phase core/shell upconversion nanoparticles as reporters for ensemble and single particle studies}, url={http://dx.doi.org/10.1039/d0nr02172e}, DOI={10.1039/d0nr02172e}, abstractNote={A set of sub-15 nm ytterbium-enriched α-NaYbF4:Er3+@CaF2core/shell upconversion nanoparticles have been developed for both ensemble- and single particle-level imaging studies, presenting a high quantum yield of 0.77% at a low saturation power density of 110 W cm−2.}, journal={Nanoscale}, publisher={Royal Society of Chemistry (RSC)}, author={Meiling, Tan and Monks, Melissa-Jane and Huang, Dingxin and Meng, Yongjun and Chen, Xue-Wen and ZHOU, YING and Lim, Shuang-Fang and Würth, Christian and Resch-Genger, Ute and Chen, Guanying}, year={2020} }
 @misc{bradac_lim_chang_aharonovich_2020, title={Optical Nanoscale Thermometry: From Fundamental Mechanisms to Emerging Practical Applications}, volume={8}, ISSN={["2195-1071"]}, DOI={10.1002/adom.202000183}, abstractNote={Abstract}, number={15}, journal={ADVANCED OPTICAL MATERIALS}, author={Bradac, Carlo and Lim, Shuang Fang and Chang, Huan-Cheng and Aharonovich, Igor}, year={2020}, month={Aug} }
 @article{lim_wirth_bravo_schuck_hallen_2019, title={Large Available Volume Particles for Enhanced Deep UV Local Raman Sensing}, volume={11086}, ISSN={["1996-756X"]}, DOI={10.1117/12.2529434}, abstractNote={The combination of resonance Raman with deep UV excitation, DUVRR, gives greater selectivity and eliminates background fluorescence, enabling sensitive detection of UV absorbing nucleotide bases and amino acids. We demonstrate this combination with our 3D nanopore structure design. Resonance Raman is specific to a molecule absorbing at the excitation, while plasmon resonance of a small, shape-, index- and size- tuned metal dramatically increases the electric field strength in the active region. The 3D nanostructure exploits nanopores that retain the advantages of small-gap antennas but increases the ease of fabrication, availability, and detection volume compared to conventional plasmon-based designs, such as gaps between two particles, by being inherently single particle, with edge enhancement open to diffusion, and by possessing a large number of pores per particle. We show the large local field enhancement (hot spots) of the pores. Comparisons with an Al and silica coated/uncoated microsphere template with/without nanopores clearly show a significant blue shift of the 280 nm peak to (the more useful) 265 nm, in the presence of a hollow sphere with nanopores. Raman measurement of Tryptophan on an aluminum nanopore structure with excitation from our tunable OPO system in the visible and deep UV region indicate visible excitation causes more fluorescence and is less specific for the tryptophan, even displaying a Raman peak at the silicon substrate, while the deep-UV Raman spectra, at an energy close to the nanopore resonance, shows no substrate signal and peaks with close correlation to the known tryptophan vibrations.}, journal={UV AND HIGHER ENERGY PHOTONICS: FROM MATERIALS TO APPLICATIONS 2019}, author={Lim, Shuang Fang and Wirth, Janina and Bravo, Angel Fernandez and Schuck, Peter James and Hallen, Hans D.}, year={2019} }
 @article{li_lim_puretzky_riehn_hallen_2018, title={DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy}, volume={114}, ISSN={["1542-0086"]}, DOI={10.1016/j.bpj.2018.04.021}, abstractNote={We show that DNA carrying 5-methylcytosine modifications or methylated DNA (m-DNA) can be distinguished from DNA with unmodified cytosine by Raman spectroscopy enhanced by both a bowtie nanoantenna and excitation resonance. In particular, m-DNA can be identified by a peak near 1000 cm−1 and changes in the Raman peaks in the 1200–1700 cm−1 band that are enhanced by the ring-absorption resonance. The identification is robust to the use of resonance Raman and nanoantenna excitation used to obtain significant signal improvement. The primary differences are three additional Raman peaks with methylation at 1014, 1239, and 1639 cm−1 and spectral intensity inversion at 1324 (C5=C6) and 1473 cm−1 (C4=N3) in m-DNA compared to that of DNA with unmodified cytosine. We attribute this to the proximity of the methyl group to the antenna, which brings the (C5=C6) mode closer to experiencing a stronger near-field enhancement. We also show distinct Raman spectral features attributed to the transition of DNA from a hydrated state, when dissolved, to a dried/denatured state. We observe a general broadening of the larger lines and a transfer of spectral weight from the ∼1470 cm−1 vibration to the two higher-energy lines of the dried m-DNA solution. We attribute the new spectral characteristics to DNA softening under high salt conditions and find that the m-DNA is still distinguishable via the ∼1000 cm−1 peak and distribution of the signal in the 1200–1700 cm−1 band. The nanoantenna gain exceeds 20,000, whereas the real signal ratio is much less because of a low average enhanced region occupancy even with these relatively high DNA concentrations. It is improved when fixed DNA in a salt crystal lies near the nanoantenna. The Raman resonance gain profile is consistent with A-term expectations, and the resonance is found at ∼259 nm excitation wavelength.}, number={11}, journal={BIOPHYSICAL JOURNAL}, author={Li, Ling and Lim, Shuang Fang and Puretzky, Alexander and Riehn, Robert and Hallen, Hans D.}, year={2018}, month={Jun}, pages={2498–2506} }
 @article{li_lim_puretzky_long_riehn_hallen_2018, title={DNA methylation detection using UV nano bowtie antenna enhanced Raman spectroscopy}, volume={10727}, ISSN={["1996-756X"]}, DOI={10.1117/12.2321283}, abstractNote={Methylation in DNA is a controlling factor in gene expression, embryonic development, and has been found to be important in infections and cancer. From a basic biology point of view, great heterogeneity has been found in methylation levels within tissues, so questions arises as to how and why. We show that methylated-DNA (m-DNA) can be distinguished from non-methylated (n-DNA) with nano-bowtie- and resonance- enhanced Raman spectra. By tuning the bowtie antenna to the resonance wavelength, both gains can be realized. Two additional Raman peaks in the 1200 – 1700 cm-1 band appear with methylation: one at 1239 cm-1 and the other at 1639 cm-1; a weak peak near 1000 cm-1 also appears with methylation. We also find that the two spectral features, although the latter with slight modification, can be used to distinguish the methylation state even when the DNA is denatured, as we show when we induce crystallization of the salts in the solution with increased excitation power, or allow it to happen naturally via solvent evaporation, and the DNA is trapped within the salt crystals. A comparison between liquid/solution to dried/denatured state m-DNA shows a general broadening of the larger lines and a transfer of spectral weight from the ~1470 cm-1 vibration to two higher energy lines. The applicability of the resonance-Raman in these spectra is shown by demonstrating that the Raman spectral characteristics hardly change as the Raman resonance in excitation wavelength is approached. Finally, we comment on real signal gain in this double-resonance system.}, journal={UV AND HIGHER ENERGY PHOTONICS: FROM MATERIALS TO APPLICATIONS 2018}, author={Li, Ling and Lim, Shuang Fang and Puretzky, Alexander and Long, Brandon J. N. and Riehn, Robert and Hallen, Hans}, year={2018} }
 @article{roushan_azad_movahed_ray_livshits_lim_weninger_riehn_2018, title={Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement}, volume={8}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/S41598-018-28278-0}, DOI={10.1038/S41598-018-28278-0}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Roushan, Maedeh and Azad, Zubair and Movahed, Saeid and Ray, Paul D. and Livshits, Gideon I. and Lim, Shuang Fang and Weninger, Keith R. and Riehn, Robert}, year={2018}, month={Jul} }
 @article{green_huang_pan_han_lim_2018, title={Optical Temperature Sensing With Infrared Excited Upconversion Nanoparticles}, volume={6}, ISSN={["2296-2646"]}, DOI={10.3389/fchem.2018.00416}, abstractNote={Upconversion Nanoparticles (UCNPs) enable direct measurement of the local temperature with high temporal and thermal resolution and sensitivity. Current studies focusing on small animals and cellular systems, based on continuous wave (CW) infrared excitation sources, typically lead to localized thermal heating. However, the effects of upconversion bioimaging at the molecular scale, where higher infrared intensities under a tightly focused excitation beam, coupled with pulsed excitation to provide higher peak powers, is not well understood. We report on the feasibility of 800 and 980 nm excited UCNPs in thermal sensing under pulsed excitation. The UCNPs report temperature ratiometrically with sensitivities in the 1 × 10−4 K−1 range under both excitation wavelengths. Our optical measurements show a ln(I525/I545) vs. 1/T dependence for both 800 nm and 980 nm excitations. Despite widespread evidence promoting the benefits of 800 nm over 980 nm CW excitation in avoiding thermal heating in biological imaging, in contrary, we find that given the pulsed laser intensities appropriate for single particle imaging, at both 800 and 980 nm, that there is no significant local heating in air and in water. Finally, in order to confirm the applicability of infrared imaging at excitation intensities compatible with single nanoparticle tracking, DNA tightropes were exposed to pulsed infrared excitations at 800 and 980 nm. Our results show no appreciable change in the viability of DNA over time when exposed to either wavelengths. Our studies provide evidence for the feasibility of exploring protein-DNA interactions at the single molecule scale, using UCNPs as a reporter.}, journal={FRONTIERS IN CHEMISTRY}, author={Green, Kory and Huang, Kai and Pan, Hai and Han, Gang and Lim, Shuang Fang}, year={2018}, month={Sep} }
 @article{wirth_green_o'connor_lim_2017, title={Enhancement of Upconverted Fluorescence by Interference Layers}, volume={13}, ISSN={1613-6810}, url={http://dx.doi.org/10.1002/SMLL.201602846}, DOI={10.1002/SMLL.201602846}, abstractNote={Upconverting nanoparticles show potential applications in the field of photovoltaics and array‐based detection devices. While fluorescence enhancement using interference of incident radiation is well known in Stokes‐shift type systems such as fluorescent dyes; the effect of such interference geometry in nonlinear Anti‐Stokes type emission, such as in upconversion rare earth photophysics is demonstrated for the first time. This work describes in detail the influence of the interference modulation on both the excitation (interion energy transfer) and radiative decay with nonradiative decay processes active between emissive levels. These effects are illustrated in the thickness dependence of the decay rate and rise time. Single particle upconverted spectra and time‐resolved measurements show concurrent optimization of the infrared absorption and emission at 540 and 650 nm, with an average enhanced emission of 20 times at λ = 540 and 45 times at λ = 650 nm, dependent on the interference layer thickness and on the excitation intensity. The experimental results are correlated with finite element modeling. Both experiments and calculations show emission enhancement at an interference layer thickness of about 740 ± 20 nm, where such tolerance and the planar design, leads to ease in implementation in applications.}, number={6}, journal={Small}, publisher={Wiley}, author={Wirth, Janina and Green, Kory K. and O'Connor, Megan and Lim, Shuang F.}, year={2017}, month={Feb}, pages={1602846} }
 @article{wirth_hallen_lim_2017, title={Influence of Gold Metallodielectric Partial-Shell Geometrical Irregularities on Dark Plasmon Resonances}, volume={121}, ISSN={["1932-7447"]}, url={https://doi.org/10.1021/acs.jpcc.7b05060}, DOI={10.1021/acs.jpcc.7b05060}, abstractNote={The geometric asymmetry of real, fabricated gold partial shells leads to orientation and gold partial coverage dependent local fields and scattering. We illustrate this with single-particle measurements and finite element calculations. In particular, we show that the position and number of well-defined protrusions on the edge of a partial shell qualitatively change the spectra. The metallic protrusions result in geometrical asymmetry, which leads to excitation of the optically dark quadrupole mode as a function of incident light excitation and polarization. The far-field scattering peaks result from the bright dipole resonance with contribution from the dark resonance in the presence of the partial-shell surface protrusions. With more dark modes, the overall scattered intensity decreases, reflecting the energy trapped in the local electric fields of the dark modes, until it ultimately dissipates in the metal.}, number={29}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, publisher={American Chemical Society (ACS)}, author={Wirth, Janina and Hallen, Hans and Lim, Shuang Fang}, year={2017}, month={Jul}, pages={15937–15942} }
 @article{green_wirth_lim_2017, title={Nanoplasmonic Upconverting Nanoparticles as Orientation Sensors for Single Particle Microscopy}, volume={7}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/S41598-017-00869-3}, DOI={10.1038/S41598-017-00869-3}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Nature}, author={Green, Kory K. and Wirth, Janina and Lim, Shuang F.}, year={2017}, month={Apr} }
 @article{green_wirth_lim_2016, title={Optical investigation of gold shell enhanced 25 nm diameter upconverted fluorescence emission}, volume={27}, ISSN={0957-4484 1361-6528}, url={http://dx.doi.org/10.1088/0957-4484/27/13/135201}, DOI={10.1088/0957-4484/27/13/135201}, abstractNote={We enhance the efficiency of upconverting nanoparticles by investigating the plasmonic coupling of 25 nm diameter NaYF4:Yb, Er nanoparticles with a gold-shell coating, and study the physical mechanism of enhancement by single-particle, time-resolved spectroscopy. A three-fold overall increase in emission intensity, and five-fold increase of green emission for these plasmonically enhanced particles have been achieved. Using a combination of structural and fluorescent imaging, we demonstrate that fluorescence enhancement is based on the photonic properties of single, isolated particles. Time-resolved spectroscopy shows that the increase in fluorescence is coincident with decreased rise time, which we attribute to an enhanced absorption of infrared light and energy transfer from Yb3+ to Er3+ atoms. Time-resolved spectroscopy also shows that fluorescence life-times are decreased to different extents for red and green emission. This indicates that the rate of photon emission is not suppressed, as would be expected for a metallic cavity, but rather enhanced because the metal shell acts as an optical antenna, with differing efficiency at different wavelengths.}, number={13}, journal={Nanotechnology}, publisher={IOP Publishing}, author={Green, Kory and Wirth, Janina and Lim, Shuang Fang}, year={2016}, month={Feb}, pages={135201} }
 @article{roushan_azad_lim_wang_riehn_2015, title={Interference of ATP with the fluorescent probes YOYO-1 and YOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels}, volume={182}, ISSN={0026-3672 1436-5073}, url={http://dx.doi.org/10.1007/S00604-015-1495-7}, DOI={10.1007/s00604-015-1495-7}, abstractNote={Intercalating fluorescent probes are widely used to visualize DNA in studies on DNA-protein interactions. Some require the presence of adenosine triphosphate (ATP). We have investigated the mechanical properties of DNA stained with the fluorescent intercalating dyes YOYO-1 and YOYO-3 as a function of ATP concentrations (up to 2 mM) by stretching single molecules in nanofluidic channels with a channel cross-section as small as roughly 100×100 nm2. The presence of ATP reduces the length of the DNA by up to 11 %. On the other hand, negligible effects are found if DNA is visualized with the minor groove-binding probe 4',6-diamidino-2-phenylindole. The apparent drop in extension under nanoconfinement is attributed to an interaction of the dye and ATP, and the resulting expulsion of YOYO-1 from the double helix.}, number={7-8}, journal={Microchimica Acta}, publisher={Springer Science and Business Media LLC}, author={Roushan, Maedeh and Azad, Zubair and Lim, Shuang Fang and Wang, Hong and Riehn, Robert}, year={2015}, month={Apr}, pages={1561–1565} }
 @inproceedings{green_wirth_o'connor_lim_2015, title={Multifunctional diagnostic, nanothermometer, and photothermal nano-devices}, volume={9584}, booktitle={Ultrafast nonlinear imaging and spectroscopy iii}, author={Green, K. and Wirth, J. and O'Connor, M. and Lim, S. F.}, year={2015} }
 @article{li_green_hallen_lim_2014, title={Enhancement of single particle rare earth doped NaYF4: Yb, Er emission with a gold shell}, volume={26}, ISSN={0957-4484 1361-6528}, url={http://dx.doi.org/10.1088/0957-4484/26/2/025101}, DOI={10.1088/0957-4484/26/2/025101}, abstractNote={Upconversion of infrared light to visible light has important implications for bioimaging. However, the small absorption cross-section of rare earth dopants has limited the efficiency of these anti-Stokes nanomaterials. We present enhanced excitation absorption and single particle fluorescent emission of sodium yttrium fluoride, NaYF4: Yb, Er based upconverting nanoparticles coated with a gold nanoshell through surface plasmon resonance. The single gold-shell coated nanoparticles show enhanced absorption in the near infrared, enhanced total emission intensity, and increased green relative to red emission. We also show differences in enhancement between single and aggregated gold shell nanoparticles. The surface plasmon resonance of the gold-shell coated nanoparticle is shown to be dependent on the shell thickness. In contrast to other reported results, our single particle experimental observations are corroborated by finite element calculations that show where the green/red emission enhancement occurs, and what portion of the enhancement is due to electromagnetic effects. We find that the excitation enhancement and green/red emission ratio enhancement occurs at the corners and edges of the doped emissive core.}, number={2}, journal={Nanotechnology}, publisher={IOP Publishing}, author={Li, Ling and Green, Kory and Hallen, Hans and Lim, Shuang Fang}, year={2014}, month={Dec}, pages={025101} }
 @article{roushan_kaur_karpusenko_countryman_ortiz_lim_wang_riehn_2014, title={Probing transient protein-mediated DNA linkages using nanoconfinement}, volume={8}, number={3}, journal={Biomicrofluidics}, author={Roushan, M. and Kaur, P. and Karpusenko, A. and Countryman, P. J. and Ortiz, C. P. and Lim, S. F. and Wang, H. and Riehn, R.}, year={2014} }
 @article{lim_karpusenko_blumers_streng_riehn_2013, title={Chromatin modification mapping in nanochannels}, volume={7}, ISSN={1932-1058}, url={http://dx.doi.org/10.1063/1.4833257}, DOI={10.1063/1.4833257}, abstractNote={We report the simultaneous mapping of multiple histone tail modifications on chromatin that has been confined to nanofluidic channels. In these channels, chromatin is elongated, and histone modification can be detected using fluorescently tagged monoclonal antibodies. Using reconstituted chromatin with three distinct histone sources and two histone tail modification probes (H3K4me3 and H3K9ac), we were able to distinguish chromatin from the different sources. Determined ratios of the two modifications were consistent with the bulk composition of histone mixtures. We determined that the major difficulty in transitioning the mapping method to site-specific profiling within single genomic molecules is the interference of naturally aggregating, off-the shelf antibodies with the internal structure of chromatin.}, number={6}, journal={Biomicrofluidics}, publisher={AIP Publishing}, author={Lim, Shuang Fang and Karpusenko, Alena and Blumers, Ansel L. and Streng, Diana E. and Riehn, Robert}, year={2013}, month={Nov}, pages={064105} }
 @article{karpusenko_carpenter_zhou_lim_pan_riehn_2012, title={Fluctuation modes of nanoconfined DNA}, volume={111}, ISSN={0021-8979 1089-7550}, url={http://dx.doi.org/10.1063/1.3675207}, DOI={10.1063/1.3675207}, abstractNote={We report an experimental investigation of the magnitude of length and density fluctuations in DNA that has been stretched in nanofluidic channels. We find that the experimental data can be described using a one-dimensional overdamped oscillator chain with nonzero equilibrium spring length and that a chain of discrete oscillators yields a better description than a continuous chain. We speculate that the scale of these discrete oscillators coincides with the scale at which the finite extensibility of the polymer manifests itself. We discuss how the measurement process influences the apparent measured dynamic properties, and outline requirements for the recovery of true physical quantities.}, number={2}, journal={Journal of Applied Physics}, publisher={AIP Publishing}, author={Karpusenko, Alena and Carpenter, Joshua H. and Zhou, Chunda and Lim, Shuang Fang and Pan, Junhan and Riehn, Robert}, year={2012}, month={Jan}, pages={024701} }
 @article{li_lim_puretzky_riehn_hallen_2012, title={Near-field enhanced ultraviolet resonance Raman spectroscopy using aluminum bow-tie nano-antenna}, volume={101}, number={11}, journal={Applied Physics Letters}, author={Li, L. and Lim, S. F. and Puretzky, A. A. and Riehn, R. and Hallen, H. D.}, year={2012} }
 @article{lim_karpusenko_sakon_hook_lamar_riehn_2011, title={DNA methylation profiling in nanochannels}, volume={5}, number={3}, journal={Biomicrofluidics}, author={Lim, S. F. and Karpusenko, A. and Sakon, J. J. and Hook, J. A. and Lamar, T. A. and Riehn, R.}, year={2011} }
 @article{carpenter_karpusenko_pan_lim_riehn_2011, title={Density fluctuations dispersion relationship for a polymer confined to a nanotube}, volume={98}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.3602922}, DOI={10.1063/1.3602922}, abstractNote={DNA confined to rigid nanotubes shows density fluctuations around its stretched equilibrium conformation. We report an experimental investigation of the length-scale dependent dynamics of these density fluctuations. We find that for highly elongated molecules a Rouse description is consistent with observations at sufficiently large length scales. We further find that for strongly fluctuating molecules, or short length scales, such Rouse modes cannot be detected due to strong mixing of fluctuation modes.}, number={25}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Carpenter, Joshua H. and Karpusenko, Alena and Pan, Junhan and Lim, Shuang Fang and Riehn, Robert}, year={2011}, month={Jun}, pages={253704} }
 @article{streng_lim_riehn_2010, title={Epigenetic Analysis of Chromatin in Nanochannels}, volume={98}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2009.12.3265}, DOI={10.1016/j.bpj.2009.12.3265}, abstractNote={Nanochannels with a diameter of about 100nm2 are a novel method for stretching DNA for genomic investigations. Such devices are implemented through standard nanolithography in fused silica. The elongation of DNA results from an interplay of steric and entropic effects. Previous applications of nanochannel stretching included sizing, restriction mapping, and observation of transcription factor binding. We show here that nanochannels can also be used to map the site-specific epigenetic state of DNA. In particular, we show here that the concept by nanoconfinement can be extended to chromatin, or DNA complexed to histones, and that the stretching is within the range expected from the de Gennes theory. We also demonstrate that the location-resolved cytidine methylation state of DNA can be mapped by specific fluorescent labeling. We will discuss the basic operation of these technique, and the application to artificial substrates with predefined epigenetic marks.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Streng, Diana E. and Lim, Shuang F. and Riehn, Robert}, year={2010}, month={Jan}, pages={600a} }
 @article{streng_lim_pan_karpusenka_riehn_2009, title={Stretching chromatin through confinement}, volume={9}, ISSN={["1473-0189"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70349311158&partnerID=MN8TOARS}, DOI={10.1039/b909217j}, abstractNote={We present a method for the stretching of chromatin molecules in nanofluidic channels width a cross-section of about 80 x 80 nm(2), and hundreds of microns long. The stretching of chromatin to about 12 basepairs/nm enables location-resolved optical investigation of the nucleic material with a resolution of up to 6 kbp. The stretching is based on the equilibrium elongation that polymers experience when they are introduced into nanofluidic channels that are narrower than the Flory coil corresponding to the whole chromatin molecule. We investigate whether the elongation of reconstituted chromatin can be described by the de Gennes model. We compare nanofluidic stretching of bare DNA and chromatin of equal genomic length, and find that chromatin is 2.5 times more compact in its stretched state.}, number={19}, journal={LAB ON A CHIP}, author={Streng, Diana E. and Lim, Shuang Fang and Pan, Junhan and Karpusenka, Alena and Riehn, Robert}, year={2009}, pages={2772–2774} }
 @article{lim_riehn_tung_ryu_zhuo_dalland_austin_2009, title={Upconverting nanophosphors for bioimaging}, volume={20}, ISSN={0957-4484 1361-6528}, url={http://dx.doi.org/10.1088/0957-4484/20/40/405701}, DOI={10.1088/0957-4484/20/40/405701}, abstractNote={Upconverting nanoparticles (UCNPs) when excited in the near-infrared (NIR) region display anti-Stokes emission whereby the emitted photon is higher in energy than the excitation energy. The material system achieves that by converting two or more infrared photons into visible photons. The use of the infrared confers benefits to bioimaging because of its deeper penetrating power in biological tissues and the lack of autofluorescence. We demonstrate here sub-10 nm, upconverting rare earth oxide UCNPs synthesized by a combustion method that can be stably suspended in water when amine modified. The amine modified UCNPs show specific surface immobilization onto patterned gold surfaces. Finally, the low toxicity of the UCNPs is verified by testing on the multi-cellular C. elegans nematode.}, number={40}, journal={Nanotechnology}, publisher={IOP Publishing}, author={Lim, Shuang Fang and Riehn, Robert and Tung, Chih-kuan and Ryu, William S and Zhuo, Rui and Dalland, Joanna and Austin, Robert H}, year={2009}, month={Sep}, pages={405701} }
 @article{austin_lim_2008, title={The Sackler Colloquium on promises and perils in nanotechnology for medicine}, volume={105}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0709499105}, abstractNote={The Sackler Colloquium entitled “Nanomaterials in Biology and Medicine: Promises and Perils” was held on April 10–11, 2007. We have been able to assemble a representative sampling of 17 of the invited talks ranging over the topics presented. Any new technology carries with it both a promise of transforming the way we do things and the possibility that there are unforeseen consequences. The papers collected here represent a cross-section of these issues. As an example, we present our own work on nano-upconversion phosphors as an example of this new class of nanomaterials with potential use in medicine and biology.}, number={45}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Austin, Robert H. and Lim, Shuang-fang}, year={2008}, month={Nov}, pages={17217–17221} }
 @article{lim_riehn_ryu_khanarian_tung_tank_austin_2006, title={In Vivo and Scanning Electron Microscopy Imaging of Upconverting Nanophosphors inCaenorhabditiselegans}, volume={6}, ISSN={1530-6984 1530-6992}, url={http://dx.doi.org/10.1021/nl0519175}, DOI={10.1021/nl0519175}, abstractNote={We show here that upconversion phosphors can be imaged both by infrared excitation and in a scanning electron microscope. We have synthesized and characterized for this work up-converting phosphor nanoparticles nonaggregated nanocrystals of size range 50-200 nm. We have investigated the optical properties of 50-200 nm nanoparticles and found a square dependence of the emitted visible fluorescence on the infrared excitation and verified that under electron excitation similar narrow band emission spectra can be obtained as is seen with IR upconversion. The viability of the nanoparticles for biological imaging was confirmed by imaging the digestive system of the nematode worm Caenorhabditis elegans, and we have confirmed using energy-dispersive X-ray analysis that the up-conversion nanoparticles can be identified in a scanning electron microscope at high spatial resolution.}, number={2}, journal={Nano Letters}, publisher={American Chemical Society (ACS)}, author={Lim, Shuang Fang and Riehn, Robert and Ryu, William S. and Khanarian, Nora and Tung, Chih-kuan and Tank, David and Austin, Robert H.}, year={2006}, month={Feb}, pages={169–174} }
 @article{riehn_lu_wang_lim_cox_austin_2005, title={Restriction mapping in nanofluidic devices}, volume={102}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.0503809102}, DOI={10.1073/PNAS.0503809102}, abstractNote={
            We have performed restriction mapping of DNA molecules using restriction endonucleases in nanochannels with diameters of 100-200 nm. The location of the restriction reaction within the device is controlled by electrophoresis and diffusion of Mg
            2+
            and EDTA. We have successfully used the restriction enzymes SmaI, SacI, and PacI, and have been able to measure the positions of restriction sites with a precision of ≈1.5 kbp in 1 min using single DNA molecules.
          }, number={29}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Riehn, R. and Lu, M. and Wang, Y.-M. and Lim, S. F. and Cox, E. C. and Austin, R. H.}, year={2005}, month={Jul}, pages={10012–10016} }
 @article{lim_friend_rees_li_ma_robinson_holmes_hennebicq_beljonne_cacialli_2005, title={Suppression of Green Emission in a New Class of Blue-Emitting Polyfluorene Copolymers with Twisted Biphenyl Moieties}, volume={15}, ISSN={1616-301X 1616-3028}, url={http://dx.doi.org/10.1002/adfm.200400457}, DOI={10.1002/adfm.200400457}, abstractNote={The color purity of polyfluorene‐based blue‐emitting polymers is often compromized by “long‐wavelength” green emission bands, attributed to polymer interchain species first and more recently to formation of emissive fluorenone defects. Here, we study the nature and the suppression of such bands via characterization of a new class of polyfluorene derivatives modified by insertion of functional groups at the bridging points (position C9), so as to increase inter‐ring torsion angles. We find that the solid‐state photoluminescence spectra of random copolymers of the modified polyfluorenes and the homopolymer display a progressive decrease of the long‐wavelength emission. Electroluminescence spectra also show efficient suppression of such bands in the copolymers with a concentration of ‘twisted' comonomer units of 40 % or greater. Quantum‐chemical calculations on model oligomers address the influence of the bridging unit on the torsion angles, and the resulting excited‐state properties; the impact on molecular packing is also explored with force‐field calculations. We conclude that increase of intra‐biphenyl torsion angles is a viable strategy for suppression of long‐wavelength emission bands in polyfluorenes.}, number={6}, journal={Advanced Functional Materials}, publisher={Wiley}, author={Lim, S.-F. and Friend, R. H. and Rees, I. D. and Li, J. and Ma, Y. and Robinson, K. and Holmes, A. B. and Hennebicq, E. and Beljonne, D. and Cacialli, F.}, year={2005}, month={Jun}, pages={981–988} }